Oh yea. You're right. Now that you mention it I start remembering stuff...
I do think you need to mod the boats to the 1st Flottilla. There was some kind of discussion about modding type IX's to the start of the war. The procedure is similar for type VII's. Unfortunately I can't point you to the thread
Maybe you can find it through search...
If you have IT skills you can edit Flottilla.cfg yourself. Basically you just copy the part about 2nd Flotilla's VIIB's to the 1st flotilla section.
Edit: I had a look at SH3Commander and apparently you can edit the files there. You don't have to mess with the files in the game.