I'm going to use Rev621 seeing how it's the latest one for example's sake.
1.) Update your database to the latest revision you want. For example, if you're on Rev590 with your custom stuff, update all relevant SQL files up to Rev621.
That would mean you would need to source in:
600_group_leadership.sql
612_instance_changes.sql
615_adventure_assassination.sql
619_Adventure_Recruiter_Flavor.sql
621_LDoNTraps.sql
2.) Then export your custom stuff. This means your custom stuff is up-to-date with Rev621. Now you're all set.
3.) Source in your new database (not your custom stuff yet!). Make sure you keep an eye on the database you're using. For example, the latest PEQ database is peqdb_1129Rev610. This means the database has all updates up until Rev610.
This means you will have to source in any additional SQL files up until Rev621 which has the following SQL updates:
612_instance_changes.sql
615_adventure_assassination.sql
619_Adventure_Recruiter_Flavor.sql
621_LDoNTraps.sql
4.) Source in all of your custom stuff, and you should have no problems at all at this point. Since you made a backup with your custom stuff with Rev621 and you're sourcing in your custom stuff that's Rev621 ready, you should be all set.
The point is to make sure your custom stuff is matching with the revision you're sourcing in so there's no data/table conflicts.
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