io: Change remove_from_flying_list() to not lock flying_transfers_lock itself

This is now symmetric with add_to_flying_list(), which was already
requiring that *callers* lock flying_transfers_lock. Updated the only
2 callers.

This also makes the code correspond better to the big comment about
locking made in 138b661f.

Also documented at the top of several functions when they require that
flying_transfers_lock already be held. Verified by code review that it's
actually the case.

This should not change any behaviour at all.

References #1410