This seems to happen every month or so. One day I just open up Cubase and all of my settings are reset. I have to reinstall controllers and choose my sound card and go into my pref and make any changes I have made. Its quite annoying. I can’t figure out why it would be doing this.
I can’t say why it happens but I do a copy of the ApplicationDataFolder regularly. I also found that if I change the colours from the default then when I load up and the colours look different then I instantly know that the prefs have gone, so I know to replace them with my backup. I should say that this happens less frequently than it a few years back so it’s getting better.
The only time this sort of thing has happened to me was after an abnormal shutdown (not necessarily a crash) which left the Prefs half-written. They then reset to default on next start up. You don’t mention crashing but maybe this behaviour will give you a clue.