GoG Galaxy just updated my version of Stellaris (for Mac) and all of my saves (to the Cloud) are gone. I am not going to cry myself to sleep over it, but I have clocked in 40+ hours of game time. Has anyone else encountered this problem recently?

The Gog verson of Stellaris doesn't have online saves (to the cloud) mate
they default to the documents folder pops file storeage

In the recent patch, Stellaris got cloud saves support.

From the changelog:

[...]

CHANGELOG Update 2.4.0.7 (09 October 2019)

General

*Added Launcher v2
*Updated all factions titans with panning light meshes. Updated vfx for Ether drakes wing attack (muzzle, projectile, hit effect)
*Caravaneer ship & station vfx update
*Added "/mute " and "/unmute " chat commands
*Cloud saving support added on GoG and Paradoxplaza versions of the game

[...]

But as ussnorway mentioned, cloud saves were not supported before. Maybe your save files are still on the location he provided?

yes mate, cloud saves have just been added by the last patch so it stands to reason that his saves from before the last patch will not be on the cloud... sorry if i was not clear

now moving forward; inside the pops_filestorage will be a folder for each of your games named by empire so my Empire is the Drack Union and "drackunion_899158119"... just grab the entire folder with all its sub files and drop them into the normal save folder i.e, the same level as pop_filestoreage

if you do this then they will show up in the normal savegame list and you can keep playing your old game

be aware that Paradox doesn't test their games will keep working after this patch so you may run into bugs but Gog players can just roll back one verson to finish their games off and then roll forward again to start a new empire