It happened to me just a couple of weeks ago, there's a thread about it somewhere.
For the time being, you're homeless. Brest is not an option until it shows, and if you go to Whillelmshaven (or however you type that!), sure, they accept you there, but you're only able to replenish fuel, and torps. That's what I did, went to Whillemshaven to say good bye to my family, and then when I went to sea again, I had Brest showing up in the map... after that, it was just a matter of moving my crew and my rusty Type VIIC through Derr Kanal all the way down to the north of France.
However, if you just stay at sea untill August 28th, you'll be fine
