I completed Witcher 3 once a long time ago with both DLCs. I have't played the game for a while, like a month or two, and I ran it today and an absolutely strange thing happened to me. There were some updates but this is fine. When I loaded my latest save I noticed that I am lacking a lot of Gwent cards (the whole Skellige deck included) as well as certain missions are still active (mostly those Gwent-related), although I'm sure I completed them. On the other hand, the "Collect 'Em All" quest is failed, due to Baron's death it says, though it should not be the case as I obtained the card from him before his demise. The same happens with saves that are ca. one month old.

Anyways, if I select a bit older save from the same play-through, everything is fine. I have the Skellige deck and the Gwent book says there are no more cards missing. Collect "Em All is also completed, which is totally bizarre. It looks like the most recent saves are corrupted in a way or overwritten... No idea but there's definitely some mess that is even hard to comprehend :D

What's more, I have some achievements locked though, as I said, I completed the quests in the game and I'm 100% sure I had those achievements. Also, I can't activate the GOG Galaxy overlay. I guess shift+tab does that?

It's not a big deal, those achievements and cards missing but there is definitely a weird issue with the Cloud saves synchronization :/