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I don't know what happened. I got Doom 2016 on gog, played it a bit, took a break, played some more, took another break, then a bit later I tried playing again and all my data was gone. It asked me to calibrate the lightning like it did when I first played, and all the save slots were empty.

I'm posting this to see if I'm the only one this has happened to, or if this might be a problem that has affected others.

This has not affected my saves on steam (thankfully). This has only affected the gog version of the game.
I noticed that as well. I started playing the game using galaxy then later when I came back and I launched it with galaxy closed the save doesn’t show up. It’s like there’s two different installs between galaxy and just launching from a shortcut with galaxy closed.
I don't have Doom (2016) installed, but Flower does that too.

Comparing https://www.gog.com/forum/flower/progress_not_saving/post10 to my installation of that game, I think you can determine the ID Galaxy uses for a given game by opening a file in the installation directory that begins goggame- and ends .info, then checking the clientId line. Then you take AppData\Local\GOG.com\Galaxy\Applications\51964741675694916\Storage\Shared\Files and replace the number with the clientId you found.

OneDrive has also created similar issues with at least one game: https://www.gog.com/forum/horizon_zero_dawn_complete_edition/saved_games_where_are_they_how_do_i_delete_some/post5
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fx4level2: I noticed that as well. I started playing the game using galaxy then later when I came back and I launched it with galaxy closed the save doesn’t show up. It’s like there’s two different installs between galaxy and just launching from a shortcut with galaxy closed.
That seems to have been the problem. Thanks!

I didn't know that could happen. I accidentally clicked launch game after it had finished installing. It opened galaxy at the same time as it started the game. I didn't know it would affect things.