Upgrade in Settings failed
I have been using the PC which I built in 2020. It ran on Pop!_OS 20.04 (focal), and worked great. However, 5 year security maintenance period of Ubuntu LTS would expire in April this year. So I decided to upgrade to Pop!_OS 22.04 (jammy). I read System 76 article on upgrading, and pushed Download button in Settings > OS Upgrade & Recovery > OS Upgrade, though I had noticed OS Recovery was missing in my PC. It failed by saying my PC does not have standard /etc/apt/sources.list and /etc/fstab. I lost some deb package sources in sources.list and sources.list.d. After some research, I found fstab and missing OS Recovery was the same issue: my PC starts up from BIOS, not from UEFI.
Backup data, and clean install Pop!_OS 22.04 (jammy)
So, I decided to backup home directory data to USB drive by using Deja-dup, clean install Pop!_OS 22.04 (jammy), and restore home directory data. It took 3 hours to backup 60GB. As restoration stopped by saying some thing like illegitimate file name, I am not sure to have restored all files, though I have not noticed any lack of files yet. System 76 documents helped me a lot.
So far, so good on Pop!_OS 22.04 (jammy)
I had to re-install applications, like R, R packages, Rstudio, Google Chrome, VS Code, and Mozc (Japanese input method). For R and R packages installation, r2u by eddelbuettel was the most helpful.
Although I had considered moving to Ubuntu 24.04 (noble), I stayed on Pop!_OS this time. So far, so good. I hope this new OS will serve me well.