Cavedude made a batch file that backs up the bots to a sql file you can source in with a new database. The id's are supposed to be in a range that doesn't conflict with existing or new npc's. Not sure why you are having issues there. The inventory and owners tables are not touched during a drop_system.sql (is that the name?) so only the npc_types needs to be backed up with CD's batch file.
I'm not sure moving them to their own table would work with the spawn code. CD?
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