I'm playing All the Mods 3 and when I place a staff that contains a spell into my internal crafting area, it will remove the spell from the staff. This happens when I don't even complete the recipe where I remove the pearl from the staff. Once placed in the crafting area it removes the spell and I am left with a staff with a normal pearl in it

Update the mod, try again.

This seems to have been fixed. If you are still having this issue with the newest version of Wizardry and LibLib, please comment on this issue.