Official comment
My speculation would be that rekordbox didn't close properly and the settings file was damaged, so when it launched again it created a new one from scratch.
You are using an outdated version (we're now at 6.5.0), so there's always a chance there was a glitch in 6.4.1 which has since been corrected.
I'd suggest that you update, re-adjust your settings (or revert to a backup if you have that enabled), and if it happens again, file an inquiry ticket here and our support team can troubleshoot further.