Bug found on SteamDeck using Prism Launcher 6.3 with a new instance of MC 1.19.2, forge 43.2.6, AutoRegLib 1.8.2-55, and Quark 3.4-393.
I can launch MC and edit quark settings, launch a game and play with no problems. When I close MC and reopen it, all quark settings are lost. The MC log says "/quark-common.toml is not correct. Correcting". This warning is in the log even when the quark settings have not been changed.
I've created the same setup on my Windows PC and cannot replicate the issue on that system, so it seems like the issue is limited to Linux/Deck.
If I manually edit the file the config loads fine and works. (I did try to make the config file read-only in an attempt to not have it be reset, but this causes a crash on launch). If the file is modified on disk before the game is launched, then the altered config applies to the game, but the content of the file on disk has been reset by the time I reach the main menu. The quark settings menu contains the changes that were in the file before the game was launched. Clicking Save Changes generates a new "/quark-common.toml is not correct. Correcting" in the MC log.
Here's my log output from launching MC https://mclo.gs/jfYalDA at the point of reaching the main menu (MC still open). I consistently get this problem on SteamDeck but not on Windows.

I have tried both using the ingame quark menu system to configure configs and editing the toml file manually in a text editor. Saving with the ingame quark menu on Deck causes another error/warning message in the log and the file isn't updated. Updating the text file manually does load the settings correctly into the game despite the file being overwritten on launch.

I've run into the same issue, and so far downgrading to Quark 3.4-389 seems to prevent this issue from happening.

this should be fixed