[DiapDealer]

Sigil's every action is predicated on the notion that the opf is entirely correct. And every action Sigil undertakes ensures that the opf stays that way. Sigil can't warn you about unmanifested xhtml files when it opens an epub, because it doesn't know they exist. It's not purposely deleting them. It hasn't made a "unilateral decision." It just hasn't loaded them. Because the opf (the boss) didn't tell it to do so when it was being parsed. What you're asking for would take a complete overhaul of how Sigil opens epubs, or a complete overhaul in how they're saved. Neither would be a trivial undertaking.