Newly cloned VM conf file disappear after update

[yanjar]

Hello

I experienced this problem 2 times and would like to see if there is solution.

I used to clone a VM for testing new stuff. There is no problem when operating inside the VM or how proxmox handle it (start stop reset etc)
But i find that the newly cloned VM conf file will be disappear after i perform a proxmox update. Only conf file inside /etc/pve/qemu-server/ is absent but the vmdisk which stored in another ZFS pool remain intact.
Other non cloned VM/CT conf file still here.


The latest history log:

Start-Date: 2025-08-06  21:56:06
Commandline: apt upgrade
Install: proxmox-kernel-6.8.12-13-pve-signed:amd64 (6.8.12-13, automatic)
Upgrade: pve-docs:amd64 (8.4.0, 8.4.1), openssh-client:amd64 (1:9.2p1-2+deb12u6, 1:9.2p1-2+deb12u7), proxmox-widget-toolkit:amd64 (4.3.12, 4.3.13), libldb2:amd64 (2:2.6.2+samba4.17.12+dfsg-0+deb12u1, 2:2.6.2+samba4.17.12+dfsg-0+deb12u2), ssh:amd64 (1:9.2p1-2+deb12u6, 1:9.2p1-2+deb12u7), libpve-storage-perl:amd64 (8.3.6, 8.3.7), libwbclient0:amd64 (2:4.17.12+dfsg-0+deb12u1, 2:4.17.12+dfsg-0+deb12u2), openssh-server:amd64 (1:9.2p1-2+deb12u6, 1:9.2p1-2+deb12u7), proxmox-kernel-6.8:amd64 (6.8.12-12, 6.8.12-13), libsmbclient:amd64 (2:4.17.12+dfsg-0+deb12u1, 2:4.17.12+dfsg-0+deb12u2), libssl3:amd64 (3.0.16-1~deb12u1, 3.0.17-1~deb12u1), pve-container:amd64 (5.2.7, 5.3.0), smbclient:amd64 (2:4.17.12+dfsg-0+deb12u1, 2:4.17.12+dfsg-0+deb12u2), pve-manager:amd64 (8.4.5, 8.4.9), libpve-common-perl:amd64 (8.3.2, 8.3.4), openssh-sftp-server:amd64 (1:9.2p1-2+deb12u6, 1:9.2p1-2+deb12u7), samba-libs:amd64 (2:4.17.12+dfsg-0+deb12u1, 2:4.17.12+dfsg-0+deb12u2), samba-common:amd64 (2:4.17.12+dfsg-0+deb12u1, 2:4.17.12+dfsg-0+deb12u2), proxmox-kernel-helper:amd64 (8.1.1, 8.1.4), openssl:amd64 (3.0.16-1~deb12u1, 3.0.17-1~deb12u1)
End-Date: 2025-08-06  21:57:04

 

[fabian]

are you running some custom scripts that mess with pmxcfs? that's the only reason I can think of for files to just "disappear"..

 

[yanjar]

are you running some custom scripts that mess with pmxcfs? that's the only reason I can think of for files to just "disappear"..

No i didn't run scripts as i always want to keep the host as simple and clean as possible.
The action i perform, which i just know that it is not the "official" way, is that I run "apt upgrade" rather than "apt dist-upgrade". Not sure if it is the cause of problem.

 

[fabian]

nothing will remove VM config files automatically when upgrading packages, no matter how you upgrade.

 

[leesteken]

Maybe a cluster with split-brain? Or bad memory (run memtest?) or drive corruption (which stores the /etc/pve database)? Anything in the logs about filesystem checks and/or repairs?

 

[yanjar]

The problem is probably due to the boot SSD. One of the symptom of SSD failure is that it fail to write new data.
It just happen when i change any VM config and it failed to save it.
After cloning the boot disk to another SSD everything works fine.