As most of you probably know, Witcher 3 creates new saves every few minutes and after a few weeks of playing I've already reached the 1GB limit for GOG cloud sync and it fails sync everytime. I have manually deleted the save files from my computer but GOG sync just restores them on my computer the next time I sync.I've tried deleting them from the save folder when the game is open too but same result. I've also manually deleted them from within the game and same result.

Has anyone faced this problem yet? It seems the cloud sync feature is pretty useless if a problem like this can't be resolved manually.

It's yet to happen to me, but this issue should be addressed ASAP. We should be able to manage our cloud saves, if the storage limit remains that low.

The proper implementation of cloud saves should have some mechanism for browsing, downloading and deleting particular saves for particular saves. Unless this is done, cloud saves, to me, appears to be more hassle than helpful.
So I am not using cloud saves at the moment.

The last way you tried is the proper way. I believe it must be done within the game, otherwise it will be assumed the saves were lost and need to be restored.

Never delete from the folders if you are relying on Cloud Saves with Galaxy. That's a typical weakness of such management systems, like with iTunes and music, or photo management software. Best not to do it manually, because in essence that's sort of like hacking or using duct tape on everything. Use the programs that are already creating and managing the documents for managing the documents.

I'm not going to say you caused problems by doing those other routes, I don't know. But if it were me, I'd give a little time (a few days?) of not messing with it at all, not even playing, and then try deleting the saved games again only from within the game. Things might clear up, or maybe not. Then I'd contact support if it didn't work the way it was supposed to work rather than ever trying to hack it through the operating system and its file management.

On the other hand, if you don't use Galaxy to play that game, then its saved games won't be synced or restored. No problem.

Except when there are 1000 saves or so and deleting them in game takes FOREVER. There are several games (The Witcher 2, for example) where I spent WELL over an hour in game deleting saves when deleting them from the folder would have taken about 1 minute. That's poor management. I don't like poor management and it defeats the purpose of cloud saving, which is ease of use and portability across systems.
Sync needs to have an option popup when syncing finds different files on the PC vs in the cloud: Restore from cloud back up, or backup local files (erasing the previous cloud back up for that game).

I've been doing a search and still cannot find a solution.
This seems to be an issue 4 years later.
I am getting this error with Phoenix Point, not any other game.
I have now manually deleted the games from within the game menu itself, which took forever, and still have the problem. It says 200 MB limit, but there are only 10 saves left. Something is broken

Same here! I manually removed a LOT of saved games from Pillars of Eternity, using the game interface so I would make sure it is not out of sync, but it still says the cloud storage is exceeded. So I don't know how to fix it, I guess I will have to manually back those up...