I’ve had this happen a couple of times now. Sublime will just rewrite my user preferences file to be the default for no real reason. Is there a way to ensure Sublime doesn’t do this?

The default user preferences file is empty. Is it deleting your user preferences?

Sometimes Sublime Text will rewrite your user preferences, which deletes e.g. comments but leaves all your preferences intact; most notably, this happens on zooming in and out (it saves the new font size). Is this what you’re experiencing?

I experience this kind of behavior each time after my package control does an upgrade of my material theme. However I am not sure if that is an issue of Sublime text or rather of package-control. Currently I have stored my preferences under an different name any copy/ paste them to get the “old” look and feel. Not best practice I guess, but it works for me.

Sublime Text provides an Api that allows plugins to persist settings permanently in settings files, including the Preferences.sublime-settings file. During the process, comments and formatting are wiped.

Same here.