I was an user of Atom and later switched to VSCode. It took me few months of weighting all the options before I made the switch. That's how much I love Microsoft -- Very little.
Don't know if they got it fixed, but there was a design flaw in Atom: Bug inside some Atom plugin (`linter-ui-default` is one of it if my memory is correct) can reset the entire Atom into it's default setting, and it happens randomly (See link 1, 2 and 3).
This problem pisses me off so much and so many times. The last time it happened, I accidentally deleted my backup configuration `config.cson` when trying to recover the setting. Yes, it is technically my fault, but no, really, it is not. So, after seeing all my life flashed before my eyes, I decided to stop living ... with Atom, I had enough.
VSCode is generally a better editor when compare to Atom. I mean, VSCode has it own issues, sure. But for me, so far those issues are mild and usually got fixed quickly.
1: https://github.com/atom/atom/issues/14922 2: https://github.com/atom/atom/issues/14909 3: https://discuss.atom.io/t/atom-keeps-losing-settings/61617 (This one was in 2018 while the other two was in 2017)