Yep, I think I have the same problem; I played at home, then played at work. I completed several quests while at work. I tried to get my work save into the cloud to continue playing at home, which didn't work; back home I had my old save file. At work, it gave me the "your local save file conflicts with the online one" message; I told it to keep the local save, which caused it to break the save file completely, both at work and at home; the kingdom is in the old file's state, but some of the quests are cleared but not completed, which looks like this:
The quest has been done with all required classes, but is not done.
If I had to guess what caused this:
-Game loads online (old) file on startup
-Game notices conflict between online and local file
-Game pops up the choice dialog; user chooses to keep local file
-Game misapplies/misloads the local file, keeping the game's current world state and applying only a part of the local save (eg: flagging quests as cleared but not unlocking the associated rewards)
-Game takes this broken world state and saves it on both the local and online save.