If you combine the Morph-O-Tool with the laser wrench from the Actually Additions Mod and then look at a block from that mod, the tool permanently becomes the laser wrench.

Yes, you can close this, it is indeed my fault.
As this is pretty old code, I am just setting the stack's NBT Tag to a completely new one when clearing the positional data that is stored instead of just deleting the actual coordinates from the NBT Tag.

I'd take it up with Actually Additions. It looks like it's setting its stack rather than modifying it.