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I made a couple small edits, mostly for easier reading with subsections.
Hope it helps some other Linux (and possibly Mac) players too!
It seems to be working a little differently for everyone, so I thought I'd share my own experience.
For me, getting the game started was a pretty simple process. I just had to select forced compatibility using Proton, and then the game worked, with my saves and everything. Just had to change framerate from 30 to 60 in Settings -> Game.
There are a few hiccups (for example, the game seems to struggle to generate mutations), but I only encountered one serious problem:
In-game sound effects are ridiculously loud. To be fair, they always were, and for some reason the game never had a "Sound Effects" slider; for that reason I have always played this game with the Master Volume all the way down to 1%. But in the beta, the sound effects are much much much louder than even the ridiculously loud sound effects in the main game! In the end my only option was to turning the volume down externally. Otherwise the game would not be playable.
Also, a little quirk: the music files were moved one level down the folder tree, and a few of the tracks' names had some letters capitalized. So I had to move a few files around to re-customize the music. Nothing serious, but I'm mentioning it just in case someone is wondering where the files went or why their custom tracks aren't replacing the beta ones.
But it's done, and I can play the game again. Already got all achievements so I can do whatever I want as casually as I want. It's gonna be fun.
Hmm... for me, installing the beta did delete some files. The original music files were deleted and some new ones were reinstalled; they aren't the same size as the old ones, and the installer didn't recognize that some of the old music files were custom before it deleted them.
It's possible that the uninstaller was even more careless and deleted anything in those new folders, including files that belonged to the game and not to Proton. But I doubt it would have deleted them all.
Try searching for "nuclearthrone.sav" and see what comes up. Some of the ones in various locations must have survived. I literally have 13 copies of that file on my SSD, though they don't appear to all be up to date (there are three different sizes).
As a general rule you should always be making backups of all your game saves. Otherwise it's practically guaranteed that you will lose them at some point.
In a large number of different places with quite long addresses.
Use the search feature on the relevant disk to find out. All you have to do is input that filename and it'll spit out every copy of it in every location.
Not familiar with Steam Deck, but it should use SteamOS which is a Linux OS. It shouldn't be particularly alien. I'm on Linux and I can see those files just fine. Maybe the OS isn't properly configured, and has been set to hide certain folders and their contents.
And not being able to find any game files at all should be impossible. At the very least you could click on the "Browse local files" option on the name of the game in your library list, which would show you some game files (though admittedly not the save files).
Right-click on the name of the game, select "Manage", then click on "Browse local files". But like I said, this isn't where the save files are located, that's the location of other game files. It's where I go to install custom music, for example.
"nuclearthrone.sav" is the file you need to search for. I don't know what search program SteamOS uses (on my system it's Catfish) but it really should be able to list all instances of that file on your disk if you ask it to search for it.