It will remove it even if the skill was added by a trigger. I haven't had problems with it.
what i'm trying to say is, if you remove a skill via the native, that a unit was given through the object editor - the skill basically becomes unlearned; any skill points you used on learning that skill becomes wasted
Wasn't that what engineering upgrade is there for? I think it replaced a spell and made you able to skill on the new one with regular skill points. Give the replaced ability the same research icon and description and nobody will notice. (Correct me if im wrong, i never actually needed this)