for steam cloud to work it needs to be on both ingame and in steam library
if you have steam cloud off ingame then steam will not sync to cloud regardless of your steam library settings, that’s because the “physical” save location switches on your computer with cloud on/off ingame
*i’ve no idea which location it uses on steam deck/proton
when you’re on your PC, with cloud on ingame and ingame, you can make steam upload to your cloud by “activating” the files by engaging with them ingame, ie load all your characters and mess around with you stash etc
^that should force steam to sync/upload to cloud upon exit
if steam don’t want to manually download clouds on deck, even if you ask it to verify game files, you can try to either reinstall and see if it pulls the save during the reinstall, or you can manually pull your cloud saves
and then manually transfer them to whatever location steamdeck is saving to
^there might be some canoodling there that has to be done if steamdeck operates the same way Grim Dawn does with cloud saves on ingame for PC
in which case you need to follow the reverse steps here (how to move saves back to cloud) at the 2nd half in this post How to - Move your saves from Steam cloud to Grim Dawn's default location. - #208 by powbam , by putting your newly manually retrieved saves in the “local” save location on steam deck, and then have the game pull them to the “cloud” save location via the ingame transfer function
*this is ofc only assuming you don’t get steam deck to proper sync/pull cloud saves on its own via some of the earlier steps mentioned