Something similar happened to me a few times before. I can’t claim I know what’s happening here, but I suspect the file system. A file gets corrupted maybe or partially deleted, I don’t know, but it sits in some limbo state of existing and not existing at the same time. Other commands spit out similar errors if you try to use them on the file.
What fixed it for me (the most recent time this happened) was booting to a live USB session and checking the btrfs filesystem with # btrfs check --repair a couple of times. Then booting back to silverblue and running # ostree fsck --delete. The update went through after that.
A big warning here though. These commands are quite risky. Attempt running them only if:
Thanks for the response. I did a rpm-ostree cleanup --rollback, and it started to upgrade without the error message. Once I restarted, I noticed the update did not stick. I tried that a few times with the same result. Now I get to another error message:
system core: pruning that ends with ‘read-only file system’ message.
I loaded a live Fedora Workstation and unlocked the LUKS partition without mounting the device at /dev/mapper/UUID and check and repaired. Found many errors. Booted back into main OS and updated, and it worked. Thank you so much. Did not want to reinstall.