A couple of things strike me.
First, no matter what the realities of the mission, it seems the Bayern's trek would be officially deemed A Failure. So it could be buttoned up and filed away in some Indy Jones states secrets warehouse somewhere. I really don't see the Powers That Be wanting to admit to a lot of the stuff dredged up on that mission, and nobody spends a lot of time snooping around Failure. I generally estimated it would be a 60%+ casualties mission, so terming it a failure and tying it all around some patsie's neck seems appropriate—some innocents' lives destroyed and dragged through the dirt. The captain, court martialed, Dreyfus style, as only the French really can. The rest is the stuff of tabloid speculation.
Second, the German reunification seems to've occurred sometime while the Bayern was away.*
Third, I like the idea of the Bayern's obsolete hulk, stripped and driveless, returned to transPentapod space and parked at the inner threshold of the first 15.5 LY gap, a station and sad monument to mankind's folly in probing the Unknown.
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*EDIT: oops, wrong about this. Weird then, all that talk of Bavaria in the module