Hello @Undearius, this issue should also be mentioned to the game's dev(s) if it hasn't been already.
To revisit this, I am still experiencing this issue here in July of 2022, on Debian Sid.
Of significant note, the logs show:
[2022-06-28 22:19:37] [AppID 212680] (ValidateCache) File '/home/warp/.local/share/FasterThanLight/continue.sav' was deleted but found on disk - marking as 'forgotten'
[2022-06-28 22:19:37] [AppID 212680] YldWriteCacheDirectoryToFile - saved to '/home/warp/.steam/debian-installation/userdata/122014770/212680/remotecache.vdf'
[2022-06-28 22:19:37] [AppID 212680] Warning: files in Cloud are from app build '4710954', we are at older build '4624838' locally
[2022-06-28 22:19:37] [AppID 212680] Need to sync from local change number '0' to global change number '10575297663823686558', but not attempting now
[2022-06-28 22:19:37] [AppID 212680] Need to upload file FasterThanLight/ae_prof.sav
[2022-06-28 22:19:37] [AppID 212680] Need to locally delete file FasterThanLight/continue.sav
So it would definitely be my suspicion that there are problems with the tracking of transient save game files with a consistent name.
Nothing extracted yet.
Your system information
Please describe your issue in as much detail as possible:
Faster Than Light's game resume feature does not work, this is do to the continue.sav file from being deleted when the game is launched.
Steps for reproducing this issue:
(Windows "My Documents\My Games\FasterThanLight\continue.sav").
(Linux "~/.local/share/FasterThanLight/continue.sav")
Workaround
Disabling Steam Cloud Sync (Right click FTL > Properties > Updates > uncheck "Enable Steam Cloud ...") stops the continue.sav file from being removed.
Here is a link to another user experiencing this issue
https://steamcommunity.com/app/212680/discussions/0/624075036490407237/