I first checked my database with kobo utilities pluggin for calibre : all was ok. I tried to store my reading position => ok for some books but not all (I can't figure out why, but at least it worked for the one I was reading, so, so far, it's ok for me). I signed out and signed in again and now the sync is working nicely, why, I must admit, will, I think, remain a big mystery...
I had read a lot of books that I was to manually reset to "finished" (I hate this and couldn't find a way to store this information in calibre, though there must certainly be a way).
So, this problem isn't one anymore for me
(at least for some time I hope)