All user configs lost on reboot into latest image

Aurora
1

I woke my system up from sleep this morning, realized that it’s been some time since I’ve rebooted, maybe a week, so I used the menu and clicked reboot. After rebooting I was greeted with the “Welcome to KDE Plasma!” message as if this was the first time install. All my flatpaks are still installed, but ALL of their settings, all my configuration changes to plasma, and all my distrobox containers are gone. Looking at sudo rpm-ostree status I see

State: idle
AutomaticUpdates: stage; rpm-ostreed-automatic.timer: no runs since boot
Deployments:
● ostree-image-signed:docker://ghcr.io/ublue-os/aurora-dx-nvidia:stable
                   Digest: sha256:12d258896d4415a205ef82418257a5c11df0efcb24eb3466c61e8dcaac9515a4
                  Version: 41.20250310.2 (2025-03-10T08:36:53Z)
          LayeredPackages: hplip-gui

  ostree-image-signed:docker://ghcr.io/ublue-os/aurora-dx-nvidia:stable
                   Digest: sha256:61750d4d0446adfa24f9f5e12c3b6a9b828f57cbaef50d47fd0479f75481505c
                  Version: 41.20250302 (2025-03-02T06:03:22Z)
          LayeredPackages: hplip-gui

I see nothing in journalctl to indicate some major fault happening.

I’m flabbergasted. It is going to take me some time to restore everything back into a working state. I have to recreate all my distrobox images, redo all my settings for Plasma.

Wtf happened? I thought user level files were never touched on updates?

EDIT: Something similar appears to have happened with Silverblue:

2

This is a strange situation indeed. There aren’t any specific services in Aurora that are designed to delete files in users’ home directories.

Is your home directory completely clean or are only some files missing? It would help to understand which files disappeared to begin to debug what happened.

Do you have any btrfs snapshots that you can recover your files from?

3

Thanks for the reply. Looking now, no, there are not btrfs snapshots that I can recover from, I hadn’t set up anything like snapper to do so, but now I guess I’ll need to going forward.

My ~/.local/bin is definitely gone, in fact I think all of ~/.local was reset. My ~/.config/ seems to be missing things for nvim but it might actually also have entirely reset. the ~/.var/ directory was likewise entirely reset.

Any thoughts as to what could have happened?

However, it looks like my .zshrc and other config files directly under ~ are still there. As are all the the folders containing things I put there, work files and the like. So my home directory was not entirely deleted, but parts of it were certainly “reset” to their state from the first install.

EDIT:
On closer investigation, many things I had in my home dir were deleted as well. Lots of directories related to work were deleted.