Not if you're smart about how you make them, and make sure you save them.
Create a new .sql file from a text document called "custom.sql" and go from there. Record your changes like this:
Code:
### Choose to use Old VP ###
UPDATE spawn_conditions SET value = 1 WHERE name = 'VeeshanOld';
UPDATE spawn_conditions SET value = 0 WHERE name = 'VeeshanNew';
### This allows the rogue epic to be equipped in the range slot ###
UPDATE items SET slots = 26624 WHERE id = 11057;
### This gives the Robe of Living Fungus regen like in the old days ###
UPDATE items SET regen = 15 WHERE id = 1268;
### Change Circlet of Shadows to Circlet of Shadow ###
UPDATE lootdrop_entries SET item_id = 14730 WHERE item_id = 29400 and lootdrop_id = 3628;
UPDATE lootdrop_entries SET item_id = 14730 WHERE item_id = 29400 and lootdrop_id = 23287;
### Change Fungi Covered Great Staff to Fungus Covered Great Staff ###
UPDATE lootdrop_entries SET item_id = 10895 WHERE item_id = 11058 and lootdrop_id = 410;
### This sets the Evil Eye in Guk to drop the Bag of Sewn Evil Eye 75% and Manastone 25% ###
UPDATE lootdrop_entries SET chance = 75 WHERE lootdrop_id = 18855 and item_id = 17354;
INSERT INTO lootdrop_entries VALUES (18855,13401,1,0,25);
### This sets Drelzna to drop Jboots ###
UPDATE lootdrop_entries SET chance = 17 WHERE lootdrop_id = 2129 and item_id = 4211;
UPDATE lootdrop_entries SET chance = 16 WHERE lootdrop_id = 2129 and item_id = 5310;
UPDATE lootdrop_entries SET chance = 16 WHERE lootdrop_id = 2129 and item_id = 7308;
UPDATE lootdrop_entries SET chance = 16 WHERE lootdrop_id = 2129 and item_id = 7312;
UPDATE lootdrop_entries SET chance = 16 WHERE lootdrop_id = 2129 and item_id = 10302;
INSERT INTO lootdrop_entries VALUES (2129,2300,1,0,17);
### Fix Rathyl's Drop Rates ###
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 555;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 23202;
### This makes the Ghoul Assassin drop the Guise of the Deceiver rather than the Mask of Deception ###
UPDATE lootdrop_entries SET item_id = 2469 WHERE item_id = 2472;
### Put the old graphic on Zlandicar's Heart ###
UPDATE items SET idfile = 'IT192' WHERE id = 26009;
### This fixes Hadden to drop the Fishbone Earring 100% ###
DELETE FROM lootdrop_entries WHERE lootdrop_id = 8235 and item_id = 13100;
UPDATE lootdrop_entries SET chance = 100 WHERE lootdrop_id = 8235 and item_id = 10313;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 8235;
### Remove all Fabled mobs ###
DELETE FROM npc_types WHERE id = 2148;
DELETE FROM npc_types WHERE id = 5134;
DELETE FROM npc_types WHERE id = 12169;
DELETE FROM npc_types WHERE id = 13118;
DELETE FROM npc_types WHERE id = 16034;
DELETE FROM npc_types WHERE id = 18105;
DELETE FROM npc_types WHERE id = 33157;
DELETE FROM npc_types WHERE id = 35163;
DELETE FROM npc_types WHERE id = 37147;
DELETE FROM npc_types WHERE id = 58057;
DELETE FROM npc_types WHERE id = 58058;
DELETE FROM npc_types WHERE id = 63091;
DELETE FROM npc_types WHERE id = 63095;
DELETE FROM npc_types WHERE id = 63096;
DELETE FROM npc_types WHERE id = 63110;
DELETE FROM npc_types WHERE id = 68246;
DELETE FROM npc_types WHERE id = 68249;
DELETE FROM npc_types WHERE id = 69135;
DELETE FROM npc_types WHERE id = 70053;
DELETE FROM npc_types WHERE id = 70069;
DELETE FROM npc_types WHERE id = 107156;
DELETE FROM npc_types WHERE id = 107157;
DELETE FROM npc_types WHERE id = 107158;
DELETE FROM npc_types WHERE id = 107160;
DELETE FROM npc_types WHERE id = 121091;
DELETE FROM npc_types WHERE id = 153148;
DELETE FROM npc_types WHERE id = 153149;
### Classic Era ###
# These queries make Lady Vox and Gorenaire less cunty #
#UPDATE npc_spells_entries SET spellid = 1356 WhERE id = 1514;
#UPDATE npc_spells_entries SET spellid = 1519 WhERE id = 1230;
#UPDATE npc_spells_entries SET spellid = 1519 WhERE id = 1271;
# These queries replace the Guardian of the Seal with Master Yael in the Hole #
UPDATE spawnentry SET npcID = 39138 WHERE spawngroupID = 10317;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 10319;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 10320;
# These queries replace the Echo of Nortlav with Nortlav the Scalekeeper #
UPDATE spawnentry SET npcID = 39148 WHERE spawngroupID = 10321;
UPDATE spawnentry SET npcID = 39148 WHERE spawngroupID = 10157;
UPDATE npc_types SET loottable_id = 1921 WHERE id = 39148;
DELETE FROM lootdrop_entries WHERE lootdrop_id = 3678 AND item_id = 67049;
UPDATE lootdrop_entries SET chance = 100 WHERE lootdrop_id = 3678 AND item_id = 5392;
### Kunark Era ###
# Fix the safe spot in Karnor #
UPDATE zone SET safe_x = 304.7 WHERE short_name = 'karnor';
UPDATE zone SET safe_y = 22.2 WHERE short_name = 'karnor';
UPDATE zone SET safe_z = 4.1 WHERE short_name = 'karnor';
# Fix the safe spot in City of Mist #
UPDATE zone SET safe_x = -857 WHERE short_name = 'citymist';
UPDATE zone SET safe_y = -1 WHERE short_name = 'citymist';
UPDATE zone SET safe_z = 4 WHERE short_name = 'citymist';
# Fix the safe spot in Chardok #
UPDATE zone SET safe_x = 926.2 WHERE short_name = 'chardok';
UPDATE zone SET safe_y = -99.8 WHERE short_name = 'chardok';
UPDATE zone SET safe_z = 104 WHERE short_name = 'chardok';
# Fix the safe spot in ChardokB #
UPDATE zone SET safe_x = -218 WHERE short_name = 'chardokb';
UPDATE zone SET safe_y = 306 WHERE short_name = 'chardokb';
UPDATE zone SET safe_z = 1.6 WHERE short_name = 'chardokb';
# Remove improper spawns from Droga #
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9052;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8910;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8890;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8909;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9055;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9028;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8919;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9049;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9043;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8870;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9048;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8916;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9054;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 47310;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9082;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9051;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9047;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9053;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9046;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8923;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8913;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9100;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9169;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8904;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 9004;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 13333;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 8867;
# Take the nameds out of Nurga #
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11231;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11212;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11202;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11279;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11280;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11277;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11218;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11272;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11237;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11228;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11225;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11194;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11315;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11238;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11149;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11165;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 11167;
# Remove improper spawns from Sebilis #
DELETE FROM spawnentry WHERE spawngroupID = 11556 AND npcID = 89139;
UPDATE spawnentry SET chance = 33 WHERE spawngroupID = 11556 AND npcID = 89003;
UPDATE spawnentry SET chance = 33 WHERE spawngroupID = 11556 AND npcID = 89004;
UPDATE spawnentry SET chance = 34 WHERE spawngroupID = 11556 AND npcID = 89005;
DELETE FROM spawnentry WHERE spawngroupID = 11655 AND npcID = 89139;
UPDATE spawnentry SET chance = 16 WHERE spawngroupID = 11655 AND npcID = 89016;
UPDATE spawnentry SET chance = 16 WHERE spawngroupID = 11655 AND npcID = 89018;
UPDATE spawnentry SET chance = 17 WHERE spawngroupID = 11655 AND npcID = 89026;
UPDATE spawnentry SET chance = 17 WHERE spawngroupID = 11655 AND npcID = 89028;
UPDATE spawnentry SET chance = 17 WHERE spawngroupID = 11655 AND npcID = 89031;
UPDATE spawnentry SET chance = 17 WHERE spawngroupID = 11655 AND npcID = 89118;
# Remove improper spawns from Chardok #
DELETE FROM spawnentry WHERE spawngroupID = 8328 AND npcID = 103085;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 8328 AND npcID = 103063;
DELETE FROM spawnentry WHERE spawngroupID = 12987 AND npcID = 103127;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 12987 AND npcID = 103063;
DELETE FROM spawnentry WHERE spawngroupID = 8327 AND npcID = 103152;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 8327 AND npcID = 103063;
DELETE FROM spawnentry WHERE spawngroupID = 12986 AND npcID = 103126;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 12986 AND npcID = 103063;
UPDATE spawnentry SET npcID = 103063 WHERE spawngroupID = 8324;
DELETE FROM spawnentry WHERE spawngroupID = 12988 AND npcID = 103128;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 12988 AND npcID = 103063;
DELETE FROM spawnentry WHERE spawngroupID = 8325 AND npcID = 103087;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 8325 AND npcID = 103063;
DELETE FROM spawnentry WHERE spawngroupID = 8376 AND npcID = 103161;
UPDATE spawnentry SET chance = 20 WHERE spawngroupID = 8376 AND npcID = 103059;
UPDATE spawnentry SET chance = 20 WHERE spawngroupID = 8376 AND npcID = 103132;
UPDATE spawnentry SET chance = 20 WHERE spawngroupID = 8376 AND npcID = 103165;
UPDATE spawnentry SET chance = 20 WHERE spawngroupID = 8376 AND npcID = 103182;
UPDATE spawnentry SET chance = 20 WHERE spawngroupID = 8376 AND npcID = 103188;
DELETE FROM spawnentry WHERE spawngroupID = 8452 AND npcID = 103161;
UPDATE spawnentry SET chance = 33 WHERE spawngroupID = 8452 AND npcID = 103011;
UPDATE spawnentry SET chance = 33 WHERE spawngroupID = 8452 AND npcID = 103149;
UPDATE spawnentry SET chance = 33 WHERE spawngroupID = 8452 AND npcID = 103171;
DELETE FROM spawnentry WHERE spawngroupID = 12978 AND npcID = 103161;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 12978 AND npcID = 103118;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 36868;
# Remove new Skyfire spawns #
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 48034;
UPDATE spawnentry SET chance = 0 WHERE spawngroupID = 48036;
# Replace Guardian Wurms #
INSERT INTO npc_types VALUES (91099,'a_guardian_wurm','',60,158,1,7,32000,2,0,1,15,5,0,4642,0,0,4597,265,530,'SEMCD',70,0,0,0,0,1,0,0,0,0,1.7,75,75,75,75,75,1,1,0,1714,0,0,-10,0,200,200,200,200,200,200,200,0,0,1,0,1,0,0);
UPDATE loottable_entries SET multiplier = 2 WHERE lootdrop_id = 8910;
UPDATE loottable_entries SET probability = 70 WHERE lootdrop_id = 8910;
UPDATE loottable_entries SET multiplier = 2 WHERE lootdrop_id = 8911;
DELETE FROM spawnentry WHERE spawngroupID = 11817 AND npcID = 91048;
DELETE FROM spawnentry WHERE spawngroupID = 11817 AND npcID = 91049;
UPDATE spawnentry SET npcID = 91099 WHERE spawngroupID = 11817 AND npcID = 91072;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 11817;
UPDATE spawnentry SET npcID = 91099 WHERE spawngroupID = 11818 AND npcID = 91049;
DELETE FROM spawnentry WHERE spawngroupID = 11819 AND npcID = 91050;
UPDATE spawnentry SET npcID = 91099 WHERE spawngroupID = 11819 AND npcID = 91049;
UPDATE spawnentry SET chance = 100 WHERE spawngroupID = 11819 AND npcID = 91099;
DELETE FROM spawn2 WHERE id = 18601;
# Fix drop rates in Chardok #
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3916;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 3908;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3907;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 3867;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3866;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 3932;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3931;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 3920;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3919;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 1537;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 12035;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 3911;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 1539;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 3904;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3896;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3903;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2052;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2053;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3945;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2095;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2088;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3929;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3946;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3918;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 3905;
# Fix drop rates in Hate #
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 12167;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 393;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 8654;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2507;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 9444;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 389;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2474;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 2464;
# Fix the drop rates on the Seb key parts #
DELETE FROM lootdrop_entries WHERE lootdrop_id = 9130 AND item_id = 11972;
UPDATE lootdrop_entries SET chance = 100 WHERE lootdrop_id = 9130 AND item_id = 19951;
DELETE FROM lootdrop_entries WHERE lootdrop_id = 5203 AND item_id = 11972;
UPDATE lootdrop_entries SET chance = 100 WHERE lootdrop_id = 5203 AND item_id = 19952;
# Fix drop chances in Sebilis #
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 410;
UPDATE loottable_entries SET probability = 50 WHERE lootdrop_id = 1843;
# Fix Veeshan's Peak access requirements #
UPDATE zone SET min_level = 46 WHERE short_name = 'veeshan';
UPDATE zone SET flag_needed = 'Trak Tooth' WHERE short_name = 'veeshan';
### Velious Era ###
# Remove an improper spawn from Dragon Necroplis #
DELETE FROM npc_types WHERE id = 123022;
DELETE FROM npc_types WHERE id = 123114;
# Fix Master of the Guard's drop rate #
UPDATE loottable_entries SET multiplier = 2 WHERE lootdrop_id = 5392;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 5393;
UPDATE loottable_entries SET probability = 100 WHERE lootdrop_id = 5394;
### Luclin Era ###
# Remove improper spawns from Grieg's End #
DELETE FROM npc_types WHERE id = 163168;
DELETE FROM npc_types WHERE id = 163169;
DELETE FROM npc_types WHERE id = 163170;
DELETE FROM npc_types WHERE id = 163171;
# Remove improper spawn from Akheva #
DELETE FROM npc_types WHERE id = 179134;
# Remove improper spawns from Acrylia #
DELETE FROM npc_types WHERE id = 154073;
DELETE FROM npc_types WHERE id = 154145;
Then, just run this .sql file after you source in the latest version of the database. It will allow you to stay current, while keeping your custom changes.
Also, take anything from the above list you want, I make sure to comment them pretty well. Just thought I'd give a good example.