You probably encountered a serious issue with cloud saves. I'm talking that you can't sync them, at least I couldn't as the Galaxy client would always crash when I tried to and the syncronization window itself states that you "can't sync local files with the cloud".

So here is how you CAN get it to work - did I just say you can't? Who am I, right?

First of all you need to get rid of your "Pillars of Eternity II" folder. Don't delete the files just move them so Galaxy can't find any local files. Should you have deleted your files as soon as you read "get rid of your 'Pillars of Eternity II' folder" 'cause you are an impatient kind of person, congratulations, you screwed up and no longer have any files to sync with the cloud. All others start your game and before you load any save replace the newly created folder on your computer with the one you'd moved before. You will still see the cloud files' state in the load menu but don't worry, the game will load the save files located on your computer. Simply hit "continue", save and exit the game. Et voilà, the client will snyc your files with the cloud.

You're welcome.