Remember that it's a
warning and not an error.
Before I added the frag warning, Sigil would silently mess things like this up in the background. You only found out later that something bad had happened.
Splitting can
result in invalid "naked," (file-less) frags if their corresponding target is missing, but Sigil never really had an issue with "naked" frags that started out valid and had valid targets before the spit operation was initiated.