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.

Yes, and GOG are very disinterested in fixing this. Lost ~50hrs of progress since last August, found-out the hard way, that it was because the pantheon save file was not saved in the cloud with the rest of the saves. You have to keep your saved games but they have a hard cap of 100 sessions, and they limit the cloud storage even more in August, I think.

When I talked with support, I got deflections from "game does not support cloud storage", when I countered this with evidence, I got the "this is a gameplay issue, please contact the developer", when I asked for a refund, since GOG sold me a defective product (a cloud save system that partially works and isn't mentioned anywhere is as defective as it can get) they left me for 2 weeks without a reply, then closed the ticket without any comment on their side. 100 Euros down the drain. Very unprofessional and dishonest behavior. I'll keep this in mind for future references.