Remote Buddy is fully featured during trial time and will never delete your preferences even if trial time is over. Remote Buddy also will save any change you make to the menu profiles.

Since Remote Buddy always saves the changes you make using the standard OS X CFPreferences API (which ensures file consistency even in case of application crashes/force quits), the only things I can think of that could cause a loss are a full system volume (preference files, which are usually written with delay and when the application is quit, can't be rewritten in that case and you may end up with an empty file), some sort of "deinstallation" or "cleanup" tool that deleted the menu profile prefs - or - manual, accidental deletion of the prefs file by the user, a power loss while CFPreferences was writing the profile to the prefs, ...

The menu profiles in particular are saved at [Your Home Directory]/Library/Preferences/com.iospirit.remotebuddy.menuprofiles.plist.. If you've already set up Time Machine on your Mac, this may be an easy way to recover a previous version of that file.

Best regards, 
Felix Schwarz