Guess what, problem solved..
My channels config had TID 7501, but the real TID is 7500.. I have no idea how this could have been changed, though? And I thought that the channel wouldn't show at all, if TID is not correct?
Anyway, with TID changed to 7500, I can enable UpdateChannels and vdr won't touch the transponder data anymore.
Still a bit odd that it updated the transponder data.. S13E does not have TID 7501 in any transponder, so where did the updated data come from?