Nothing beside the database and doctrine folders is changed, uninstall script should return game to the state it was at the moment when you run backup script. There is no need to delete anything manually, all important files are overwritten, and additional files does not interfere with anything.
But it's good to have original database and doctrine folders archived somwhere anyway, just in case. Deleting them in game folder and restoring clean versions from archive should solve everything, but uninstall script should work as well, even though some additional files are left there. Simple additional "delete *.*" line in the uninstall script would make the same, maybe I add in later, just in case... You may manually delete contents of doctrine and database folders and then copy to them files from .LwAmiMod folders.
But the most probably cause, as was said, is that your database files were not standard already when you run the backup script.
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