@noneshallpass I was going by what it says on page 61 of the Rule Book. It doesn’t say anything about waiting until later to send them home. I would think that would be problematic because there could be some dispute over which ships came from the French navy and which didn’t later in the game, which in real time could be a day or 2 later.
As far as sea zone 49 that refers to ships that rolled Vichy. The question asked here was about the ships that rolled German. Those stay where they are or go to their home country.
Stating that they can send the ships home under the French flag just means that in real terms that this is the justification for moving them to your home country without being intercepted by the Allies (known as a Flag of Convenience), and that you’re not moving them with magic or something stupid like that. You don’t actually have to move them along the board until you get home while making little steamboat noises. You just pick them up and move them after replacing them with German ships. You can move all of the ships that rolled Axis, some of them, or none of them.