Pantheon and custom factions are not saved via cloudsync; so a player can loose all progress if he is counting on cloudsave to save his progress between installs.

Normal game saves are working as intended.

This can be replicated by:
1) Having at least one hero in the pantheon; at least one point spent; at least one custom faction created and saved and (ideally) a game in progress
2) Close the game and make sure cloud sync happened correctly.
3) Uninstall the game and also manually delete C:\Users\<USERNAME>\Documents\Paradox Interactive\Age of Wonders 4 if the uninstall process did not do it for you
4) Reinstall the game
5) Check that:
a. Your current game progress and previous saved are restored from the cloud sync
b. Your pantheon is now empty (no heroes, no points spent; etc)
c. Your custom factions are gone

https://forum.paradoxplaza.com/forum/threads/gog-cloud-save-does-not-save-pantheon.1629061/

So AoW4 does not support cloud saves on GOG (even though some stuff will be saved on the cloud, like your actual save games); and the devs will not implement it.

So just another case of a game being inferior in GOG compared to other platforms.