I did some more tests, found a workaround, and maybe some clues to where this issue might come from. The screenshot shows three cases:
Midi Track inside of a Test Folder
Midi Track outside of a Test Folder
Midi Track duplicated so there is one inside and one outside of the Folder
These Tracks have been exported as Track Archive and the screenshot shows the reimport processes and their result. The third one is my workaround, I only have to delete the duplicated tracks after the import. I prefer this over the second method, as i can import the folder and its name & color and do not have to move tracks around (which sometimes gives weird results, in my real case screnario i have some track instruments alongside the MIDI tracks in these folders).
Of course i can provide the track archives as files if wanted, but at the moment i cannot upload them to the forum (I think?)
I have done some examination of the XML files. The Expression Maps are definitely saved within all three variations! What gets lost is only the assignment to the correct MIDI track. So hopefully it is not a long way left to go (at least for this problem, there are some more, but these are a different story and I managed to get around them by editing the XML FIiles manually).
Thanks for your attention!