Yes, charms are permanent.
Since you didn't return Tagos' axe, I think you can stash it in the battle tower chest... if you didn't try that already.
If you don't need the recipe, unenchanting equipment doesn't do anything for you, and I'm pretty sure it reduces the sell price.
For the bugged attack (most common with Ba'al, Laiken and the flying fortress generals: Ba'al. The Impossible foe?
), some people reported it working fine if they left, did other things for a while and went back, or even just reloading the same save the next day and trying again.