Thanks.
It seemed that iCloud still had some data in the sync store.
Deleted everything again, restarted DT3. Now busy uploading (still not sure it ever told me “preparing items for iCloud”).
Will report back after upload is done, whether it helped fixed my initial issue. Too bad I did not see this thread before as this is exactly my problem which confirms I am not alone with this strange behaviour.
As @Hens is writing in his comment I also never observed this strange upload behaviour, in my case never before DT 3.5.