You're updating it all wrong. The instructions are in the PEQ readme file in the order you need to source everything in. What it looks like you're doing is sourcing in the SVN files before sourcing in the database which is basically blanking out the tables in mysql.
Quote:
Initial Setup:
1. Unpack peqdb_1129Revxxx.sql.gz using winrar, gzip, whatever you use.
2. At a MySQL command prompt or GUI like Navicat source peqdb_1129Revxxx.sql into your database.
3. Source in the file load_player.sql.
4. (Optional) If you wish to use the EQOffline system, source in load_bots.sql.
For information on creating a new database see the EQEmu forums: http://eqemulator.net
Update Setup:
1. (Optional) If using EQOffline, run the bot_npcs.bat file, or bot_npcs.sh if using Linux.
2. Unpack peqdb_1129Revxxx.sql.gz using winrar, gzip, whatever you use.
3. Source drop_system.sql.
4. Source the new peqdb_1129Revxxx.sql into your database.
5. (Optional) If using EQOffline, source bot_npcs.sql.
6. Enter the updates folder, read the readme.txt there and be sure to source in any updates since the last time you updated.
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Just source in drop_system.sql from Step #3 under "Update Setup" and you should be fine.
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