Remote Buddy has no code capable of deleting its own preferences. Since it saves its preferences in the default location using the standard OS X API for preferences, it can, however, be affected by shortcomings of this system like any other application. One of these shortcomings that I experienced often with Apple Mail in the past is that, when your hard drive is full, and the preferences file is rewritten by the OS X preferences subsystem, it can end up empty and your settings are lost.

Your Remote Buddy menu preferences are stored at ~/Library/Preferences/com.iospirit.remotebuddy.menuprofiles.plist. To restore that file, quit Remote Buddy, then use Time Machine to restore the file - or copy it over from another backup you have.

Best regards, 
Felix Schwarz