Getting "Read-Only File System" Error everywhere after updating any flatpak

Bazzite
1

I’m not sure if this is a bug or something I’ve done wrong, but I wanted to check if anyone else was experiencing this or knew what was up before escalating a bug on GitHub

I noticed anytime I update any flatpak package (through the UI, through the terminal, or through ujust update ) the whole root filesystem appears to become read only:

[username]@Nemesis:~$ flatpak update org.musicbrainz.Picard
Looking for updates…


        ID                                                Branch      Op     Remote      Download
 2. [✗] org.musicbrainz.Picard.Locale                     stable      u      flathub      < 2.2 MB (partial)
 3. [✗] org.musicbrainz.Picard                            stable      u      flathub     < 22.5 MB

Warning: Unable to remove old checkout: Removing /home/[username]/.local/share/flatpak/.removed/org.kde.Platform-4d49c450514df9f8cfa5fe1a83b9e5cebe1fc2c9b958e8cabe4b1a23f4068d7c: unlinkat(look): Read-only file system
Warning: Read-only file system
Error: Read-only file system
Updates complete.
error: There were one or more errors

Soon after, just about every application starts to throw errors, such as Dolphin:

Configuration file "/var/home/[username]/.config/dolphinrc" not writable.
Please contact your system administrator.

And errors even pop up when trying to open the restart menu on the computer:

Configuration file "/var/home/[username]/.config/ksmserver-logout-greeterrc" not writable.
Please contact your system administrator.

If I were to try and update through ujust update all the following steps would throw similar errors (brew, rustup, etc). In fact, I first noticed the issue because I ran ujust update, noticed that there was a new deployment, but it wasn’t an option to boot into after this read-only filesystem error appeared. I had to run rpm-ostree upgrade separately and then reboot into the new deployment. Unfortunately this issue still persists.
Even trying to save txt files of the logs to write this report would fail unless I wrote them to a separately mounted drive

The system seems completely stable as long as I don’t try to update any flatpaks, and my laptop running Aurora doesn’t have this issue, so I’m not sure if the issue lies with Bazzite, or Flatpak, or something else.

I’m running the latest bazzite-nvidia image

State: idle
Deployments:
● ostree-image-signed:docker://ghcr.io/ublue-os/bazzite-nvidia:stable
                   Digest: sha256:d109e30673c243e8826b1053674317800a607f89ce08ccfa4eab5e6537478b36
                  Version: 41.20250216.1 (2025-02-17T16:40:17Z)
          LayeredPackages: virt-manager
                Initramfs: regenerate

Any help would be greatly appreciated!

2

Update, this was a BTRFS issue, nothing to do with Bazzite or flatpak

I learned if the whole drive goes read-only, its usually a BTRFS problem

3

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