$ ./GOG\ Games/Mana\ Spark/start.sh
Running Mana Spark
Set current directory to /home/murks/GOG Games/Mana Spark/game
Found path: /home/murks/GOG Games/Mana Spark/game/ManaSpark.x86_64
Mono path[0] = '/home/murks/GOG Games/Mana Spark/game/ManaSpark_Data/Managed'
Mono config path = '/home/murks/GOG Games/Mana Spark/game/ManaSpark_Data/Mono/etc'
Preloaded 'ScreenSelector.so'
Preloaded 'libCSteamworks.so'
Preloaded 'libfmod.so'
Preloaded 'libfmodstudio.so'
Preloaded 'libgvraudio.so'
Preloaded 'libsteam_api.so'
Unable to preload the following plugins:
libfmodstudioL.so
Player data archive not found at `/home/murks/GOG Games/Mana Spark/game/ManaSpark_Data/data.unity3d`, using local filesystem
./GOG Games/Mana Spark/start.sh: line 16: 2430 Aborted (core dumped) ./"ManaSpark.x86_64"

I can attest to this. I'm getting the exact same issue.

I installed the latest version as of today and it worked, except when I quit the game and restarted it all progress was gone.

I figured out what was going wrong, mostly.
The devs over time had renamed their save location, it is a total mess.
I had "~/.config/unity3d/Behemutt/Mana Spark" as well as "~/.config/unity3d/Behemutt/ManaSpark".
After removing that and restarting the game it was recreated as "~/.config/unity3d/BEHEMUTT/ManaSpark".
And I guess that their saving code is not case sensitive while their loading code is, or something like that, presumably. So the game seemed to be able to save but unable to load.
Most of that (except the space between words difference) won't show up on Windows because of the case insensitive file system.

So yeah, it's a mess. If you have the same issue you may be able to salvage it by renaming.
I still had some issues were config saving was unreliable, it forgot the music volume setting or didn't recognize the controller, but that seems to work now after a few attempts. No clue where that came from.

Can confirm on Linux that game saving did not work. hollunder's fix solved the issue.

I had (still have) Mana Spark 0.4.18 demo installed, which probably explains where the `~/.config/unity3d/Behemutt/ManaSpark` directory came from.

I deleted the Behemutt folder, and the game created a BEHEMUTT folder and now saves and restores my game.