Hi Peter!
Thank you very much for that overview and the warm welcome! All in all, it still remains a riddle...
At least, the brute force method of editing my save games just worked fine.
I stay offline all the time and whenever the tonnage bar does not count, I edit my last save manually. Just feels like completion of a achievement form for the BDU.
Can you imagine how it was sinking the Queen Mary during the British supplies mission and the tonnage bar didn't move at all

Now I nearly completed the mission by sinking just one ship...
Thanks for your help!