Well, if playing historically is important to you, the first U-Boat to dock in France was U-30 (VIIA) on July 7th 1940. The first IXB to dock in France was U-65 (I think) a month or so later. Most of the IXs and IXBs first started showing up in September and after.
As far as gameplay is concerned, I believe you're able to dock at any Naval Base as soon as it turns blue on the Strat Map. If its before the game recognizes the Flotilla change over, then you'll be treated as simply "in another base".
I do know that in my set up (GWX and SH3 Commander) I get an in game radio message at 00:00 the date my Flotilla officially changes over to the new base.
Hope it helps....
T
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