I don't know if the problem would reoccur with later act transitions. Contact the mod author, and if they are still updating the mod, it could be fixed by then, if it is a problem with the mod itself. If it is related to the issue that causes the problem with the storage chests, it may need to wait for a future game update.
Should the lost skills not be restored when you re-enable the mod?
If not, let me know how much it would cost to rebuy them, and I can add that to your latest act 2 save.
