Steam Cloud overwrites save after launching games on Linux with no prompt.

[TolianTaro]

System information

• Steam client version: 1747701111
• Distribution: Linux Mint 21.3
• Opted into Steam client beta?: No
• Have you checked for system updates?: Yes
• GPU: Nvidia 4080 Super

The Issue:

Launching a Proton game for the first time on Linux in a dual boot setup silently overwrites the existing Steam Cloud save with a blank save, without showing a sync conflict prompt or any warning.

This caused me to permanently lose my original Windows save data for Holocure, and Clair Obscur: Expedition 33.

Steam Cloud shows as "up to date" at all times, even after overwriting a populated cloud save with a fresh empty one.

Steps for reproducing this issue:

1. Dual boot with Windows (with working game saves via Steam Cloud).
2. Install Steam on Linux and launch a game like Holocure or Clair Obscur via Proton for the first time (no save file present yet).
3. Steam Cloud syncs an empty save as the new latest version without asking.
4. Relaunching the game on Windows shows the save data is gone — overwritten with the empty state from Linux.

What should have happened?

Steam should:

• Prompt the user when syncing a blank or new save over an existing populated cloud save.
• Preserve the Cloud save on first launch if no local save exists yet.
• Provide conflict resolution before sync occurs, not after.

What I will do now

I am in the process of fully migrating to Linux only. Once set up, I will re-test the same situation (starting with a working cloud save and launching on a clean Linux system). This will help confirm if the bug is tied to dual boot sync behavior or to Proton’s prefix handling more broadly.

[TolianTaro]

Update: Even with a clean Linux install it is still the same. installing and opening certain games on steam will erase old save data and it boot as if new across systems not only with dual-boot.

[TolianTaro]

Update/Fix Summary for Others Facing Similar Cloud Sync Issues (especially after reinstalling Linux):

figured out that the issue wasn’t with Steam on Linux itself, but with how Steam Cloud behaves when:

• A game doesn’t properly sync .sav files to the cloud

• Steam reports “Up to date” even when no save data is actually stored

• The cloud sync may only upload configs (like settings.vdf) unless the game’s Steam Cloud config explicitly includes the real save path

Key findings:

• Steam client’s “0 bytes stored” in Properties can be misleading. Always check the real cloud sync status here: https://store.steampowered.com/account/remotestorage

• SteamDB can show what a game is configured to sync. If the save path or extension isn't tracked properly files may never upload.

• If a save wasn’t uploaded before wiping/reinstalling your system, it’s lost unless manually backed up.

Fixes & Preventative Steps:

• Always confirm cloud sync is enabled globally and per-game before playing

• Let Steam finish syncing after playing—don’t shut down instantly

• Back up your userdata/ folder periodically

If using dual-boot, be careful not to create local/cloud mismatch conflicts. This won’t recover lost saves, but I hope it helps others avoid what I went through.