I was going to replay the back half of Pillars of Eternity to make different choices after a long while and since the game kept telling me I was exceeding the 200 mb limit I went and deleted some old saves both from the PC and this page:
https://www.gog.com/account/cloud-saves/

The main issue is that the old saves on the cloud keep returning so the new saves won't upload, GOG Galaxy would just stay there for a few minutes and then tell me there is not space anymore on the cloud, even though I tried countless times to delete them.

I also tried with another game which is close to the limit, Rebel Galaxy Outlaw, by deleting a few video captures (which have been included in the cloud saves for some reason) and the result is the same, it seems the server can't tell the new folder with a few files less is actually the old folder and tried to upload it on top of the old cloud backup instead of just syncing them.

Is there a solution?

Cloud saves sync every time you start or quit a game.
You can disable cloud saves in galaxy,
cogwheel (upper left corner) -> settings -> Game Features -> untick cloud saves.
Now you can delete the saves on your PC and the cloud and then if desired
re-enable cloud saves.

Yeah, I knew that, but apparently the trick is doing the deletion when the game is running because otherwise it will sync back everything on startup. I didn't so much want to get rid of cloud saves but being able to use them again after deleting enough of them to leave space on GOG's cloud storage.

Meanwhile I managed to get the GOG save manager to delete the backup saves and reuploaded the slimmed down save list for both games.

POE apparently had a bunch of backup saves from an update that did a bunch of changes back when I paused the game for about a month, RGO was mostly screens and footage taken with the in-game keys instead of overlays, mostly by accident so deleting those was a no brainer.