Sorry to hear that.
Can't say for certain, but sounds like a bug we are aware of (and should be fixed for next patch) where, in some very specific circumstances, giving a new order for a fleet triggers a check that for some reason deletes the ships.
Can't say for certain, but sounds like a bug we are aware of (and should be fixed for next patch) where, in some very specific circumstances, giving a new order for a fleet triggers a check that for some reason deletes the ships.