You would lose the mutation itself, the gene coding saying you should have that part, the “trait”, but the side effects of its removal, such as scarring would be permanent unless you got say, the pretty mutation which might get rid of scarring.
Phantom limb pain would go away if the limb comes back, is replaced with a sophisticated prosthetic, or the mutation is removed (the nerves changed when your genes changed).
Ex: your tentacle legs are amputated and replaced with cybernetic prosthetics. The phantom pain would disappear because the brain is now able to receive input it was missing.
If you did cut off an unpurifiable mutation, it is still only a physical change, your genes still have the mutation. No getting out of it that way.
Are there any unpurifiable limb or extraneous mutations that aren’t vital or inaccessible? I was thinking this would be for small or extra stuff like claws, horns, tails, etc. Unless prosthetic limbs get implemented, cutting off those hooves or tentacle legs would not be possible.