My Dwarven cleric of Dumathoin has metal domain and everything was working fine untill the last reset. Now my persistant blade and flame weapon spells have been replaced with the sixth level arcane spell Acid Fog. I have not been memorizing it since that would be a flagrant abuse of a bug, but I would like to be able to get my persistant blade and flame weapon spells back in my book.

I made a cleric of Dumathoin to test this out, and it works fine for me.

I am pretty sure that you won't actually be able to cast Acid Fog -- it's just a placeholder.

Check to make sure that you still have the right domains.2da override. If you don't, that would explain the issue.