Run the following queries, replace 279 with the proper zone ID, and abysmal with the proper zone name. This applies to the larger IDs... In this example Abysmal is ID 279, so the ranges are 278999-280000. If you wanted to delete Misty which is ID 33, the range would be 32999-34000, and so forth.
Code:
delete from grid where zoneid='279';
delete from grid_entries where zoneid='279';
delete from spawn2 where zone='abysmal';
delete from spawngroup where id >'278999' and id <'280000';
delete from spawnentry where npcid >'278999' and npcid <'280000';
delete from npc_types where id >'278999' and id <'280000';
delete from merchantlist where merchantid >'278999' and merchantid <'280000';
If you want to keep the NPCs, obviously you'd omit npc_types and ideally, merchantlist.