[Roanon]

I have seen something similar, a large number of ships disappearing in a fleet AFTER it had moved. Replay log, they were there, end of replay, vanished.
What had happend is that these ships have been cloaked by the player on that turn, being retrofitted to cloakable the turn before. It seems that though cloaking happens immediately when giving orders, in reality it happens (sometimes? always?) after moving.