I am not exactly a veteran skipper, but in a similar circumstance, I did what you seem to have done, and it worked for me.
I received a message mid-patrol that my base was changed from Wilhelmshaven to Brest, but Brest was not on the map. Having enough fuel to explore, I set course for where Brest should be. Upon arriving, all was as it should be - docks, factories, pens, were all sitting there. And a I was given the option to "Dock at Brest".
So, after double checking to be sure you have the location correct, I would try for another French port. I have read that if you end your patrol at sea, you lose credit for the tonnage sunk. Perhaps someone can confirm this for you.
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