Changing mods often causes 3 copies of the current engineer to be added as items to inventory. They can't be removed via Incenerator or Schall Uncraft.
Ah that's interesting, thanks for the report. I can't actually replicate it, but I can guess why it is happening, so I'll put some more checks in to remove the items if they are found.
For now, just put them in a chest and press c on the chest to destroy it :)