Script out all changes made to your database. When a new version is released, simply re-run your custom script to source in all of your changes. Perl changes may be more of a hassle, but you would likely just need to merge in changes from the svn (should do most of it automatically, but you would need to manually resolve conflicts). In reality, this should be done anyway, as manually changing values in live databases is not a good practice to get into.
Or, if you feel comfortable, run updates as they occur and merge them in with your changes. This is problematic when PEQ releases a new version of their DB with new npcs, items, etc.
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