Official rules don’t really address human error, and this sort of thing must be dealt with diplomatically based on your group unless you have some sort of tourney rules that address eff-ups.
If it were my house, the transport is VERY dead. It was a combat move which results in combat. it was a defenseless transport. There is no rolling required. The fact that it was left on the board is moot (to me). It’s dead. It was meant to be dead. The game isn’t technically supposed to advance to noncombat until all combats have been rolled. It’s dead. No way I’d let that float - it was a combat move specifically against it and EVERYONE knew what was going on there. The UK can’t just sit there and twiddle their thumbs hoping Germany forgets to resolve. But that’s why you should always use the combat board.
As for the French/Japan diplomatic status… That’s also part of the game. If Japan hasn’t declared war on France, hasn’t invaded FIC, hasn’t smashed the french units in any way… Well, it’s on France to think as to why that may be. That said, if France was a new player who hadn’t ever dealt with AA1940 diplomatic rules, well, then let France say, “ok, wait, it’s turn 4. Had I known that, I would have had France declare war last turn”. And then let japan revise their combat move if they want.