Actually, Brest missing on the map is a known bug in the stock game..
wouldn't be too sure with GW as i've never ever experienced it again after modding the org game with it.
Anyway, head out to Brest anyway and once you're close enough you can end the mission as normal.
As for the transfer, SHIII requires a number of patrols with each flottilla before a transfer is possible/approved so just after receiving your transfer orders you can't go back this way.
BTW.. after starting out of Brest again for your next mission the map problem is no longer an issue