I am new to PureOS and new to Gnome. I have prior Debian (and other gnu/lniux distros) but command line only.
I went through the setup wizard without any problems.
The next thing I wanted to do was ensure that I had all the latest updates, especially security updates.
When I found the Software app and navigated to Updates tab, I was seeing errors about devices and downloads, eventually saw an error to the effect of timeout starting a service.
Perhaps I was bit to eager to get going, and I dropped to a terminal and did “sudo apt update” followed by “sudo apt upgrade” a few times, and received many updates and restarted several times.
Have I possibly screwed up the Software | Updates functionality by going around the desktop to do package updates?
Which is the right way to do it on a new Librem Mini v2 - via Gnome Software app or via CLI?
I don’t think you need to worry about that, if all you did was “apt update” and “apt upgrade”, that should not have screwed up anything.
I’m sure it’s supposed to work using Gnome Software already from the start, but clearly in your case something was not working. Maybe the Software app itself had a bug and needed an update to start working correctly, in that case going to the CLI like you did was a good solution.
At least my understanding of how those things work is that Gnome Software seems to act like a kind of graphical wrapper that behind the scenes is doing pretty much the same thing as you would do using apt CLI commands, so it should be mostly OK to mix. Maybe Gnome Software can get a little confused if you run CLI commands at the same time when Gnome Software is trying to do something, but I don’t think that should be worse than what you get if you run apt commands from different terminal windows. One of them could complain that another process has locked something, things like that, but nothing dangerous.
In summary: don’t worry, be happy, and give Gnome Software another chance if you feel like it.