Are updates being done by the OS automatically or are you going into the terminal and running an apt-get upgrade periodically?

I’ve had issues when I do a terminal update because I believe that Pop expects you to do an apt-get dist-upgrade

I migrated from Joplin to Obsidian a year or two ago. It was straightforward. With Joplin, I had to use the export functionality from the desktop app. That cleaned up any non-standard bits and allowed for a straightforward import into Obsidian.