[Bug]: bottle.yml unexpectedly becomes empty (0kb)

[Veraxus]

Describe the bug

Occasionally, when I start Bottles, one of my Bottles will be missing from the GUI. When I look at the bottle directory, I can see that the bottle.yml file is empty (0kb). I'm not sure how or why, but bottle.yml is being cleared out.

This has now happened to me 4 times and I have been unable to figure out a root cause. I have started backing up bottle.yml for when this inevitably happens, as restoring that file from the backup brings everything back.

In case it's relevant: I make heavy use of a Bottle that has Epic Game Store, which is installed via the built-in Installer. I use it primarily to run Unreal Engine for development. Other than the fact that I use this Bottle frequently, there is nothing particularly notable about it. I've included the latest functional bottle.yml below.

Arch: win64
CompatData: ''
Creation_Date: '2026-06-02 19:19:24.348777'
Custom_Path: false
DLL_Overrides: {}
DXVK: dxvk-2.7.1-17-8ee652a
Environment: Gaming
Environment_Variables: {}
External_Programs:
    ceff4adc-db4e-49e4-ad7c-d9d40c92d7dc:
        arguments: -opengl -SkipBuildPatchPrereq
        executable: EpicGamesLauncher.exe
        id: ceff4adc-db4e-49e4-ad7c-d9d40c92d7dc
        name: Epic Games Store
        path: C:\Program Files (x86)\Epic Games\Launcher\Portal\Binaries\Win32\EpicGamesLauncher.exe
Inherited_Environment_Variables:
- DBUS_SESSION_BUS_ADDRESS
- DISPLAY
- HOME
- LANG
- LC_ALL
- LC_CTYPE
- LC_MESSAGES
- MANGOHUD_CONFIG
- PATH
- PULSE_SERVER
- TERM
- TZ
- USER
- WAYLAND_DISPLAY
- XAUTHORITY
- XDG_RUNTIME_DIR
Installed_Dependencies:
- d3dx9
- msls31
- arial32
- times32
- courie32
- d3dcompiler_43
- d3dcompiler_47
- mono
- gecko
- riched20
- andale32
- arialb32
- comic32
- georgi32
- impact32
- tahoma32
- trebuc32
- verdan32
- webdin32
- allfonts
- vcredist2015
Language: sys
LatencyFleX: latencyflex-v0.1.1-2-3bc9636
Limit_System_Environment: true
NVAPI: dxvk-nvapi-v0.9.1
Name: Epic Games
Parameters:
    custom_dpi: 96
    decorated: true
    discrete_gpu: true
    dxvk: true
    dxvk_nvapi: false
    fixme_logs: false
    fsr: false
    fsr_sharpening_strength: 8
    fullscreen_capture: false
    gamemode: false
    gamescope: false
    gamescope_borderless: false
    gamescope_custom_options: ''
    gamescope_fps: 0
    gamescope_fps_no_focus: 0
    gamescope_fullscreen: true
    gamescope_game_height: 0
    gamescope_game_width: 0
    gamescope_scaling: false
    gamescope_window_height: 0
    gamescope_window_width: 0
    latencyflex: false
    mangohud: false
    mangohud_display_on_game_start: true
    mouse_warp: true
    obsvkc: false
    pulseaudio_latency: false
    renderer: gl
    sandbox: false
    sync: ntsync
    take_focus: false
    use_be_runtime: true
    use_eac_runtime: true
    use_runtime: false
    use_steam_runtime: false
    versioning_automatic: false
    versioning_compression: false
    versioning_exclusion_patterns: false
    virtual_desktop: false
    virtual_desktop_res: 1280x720
    vkbasalt: false
    vkd3d: true
    vmtouch: false
    vmtouch_cache_cwd: false
    wayland: false
    winebridge: false
Path: Epic-Games
Registry_Rules: []
Runner: proton-cachyos-11.0-20260519-slr-x86_64
RunnerPath: ''
Sandbox:
    share_net: false
    share_sound: false
State: 0
Uninstallers: {}
Update_Date: '2026-06-02 19:23:37.565105'
VKD3D: vkd3d-proton-3.0.1-1-34ab1ce
Versioning: false
Versioning_Exclusion_Patterns: []
Windows: win10
Winebridge: false
WorkingDir: ''
data: {}
run_in_terminal: false
session_arguments: ''

To Reproduce

1. Run the application.
2. Restart the Bottle a few times, reboot a few times.
3. The Bottle disappears from the GUI and bottle.yml is empty.

Package

Flatpak from Flathub

Distribution

CachyOS

Debugging Information

Official Package: true
Version: '64.0'
DE/WM: plasma
Display:
    X.org: true
    X.org (port): :0
    Wayland: true
Graphics:
    vendors:
        amd:
            vendor: amd
            envs:
                DRI_PRIME: '1'
            icd: /usr/share/vulkan/icd.d/radeon_icd.x86_64.json:/usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/radeon_icd.x86_64.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/radeon_icd.i686.json
    prime:
        integrated: null
        discrete: null
Kernel:
    Type: Linux
    Version: 7.0.6-1-cachyos
Disk:
    Total: 33469075456
    Free: 33468907520
RAM:
    MemTotal: 62.3GiB
    MemAvailable: 55.1GiB
Bottles_envs: null

Troubleshooting Logs

Additional context

This appears to happen primarily after the computer has been freshly started / rebooted. I'm starting to pay attention to how Bottles shuts down before I turn off the computer, and will add to this report if I find any new clues.