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Thanks for asking.
Remote Buddy's preference files have no influence on whether or not an application turns up in the Preferences. Remote Buddy doesn't offer any option for this.
Whether or not an application turns up in Remote Buddy's Preferences depends on whether OS X Launch Services knows an application with the respective bundle identifier at launch time.
So when Remote Buddy asks OS X during launch "Where can I find Plex?" and OS X returns "Not on this system", it won't turn up. If it is installed and registered with Launch Services (usually by launching it once), OS X will return "Hey buddy, you can find it in /Applications/.…" and Remote Buddy will make it available in its Preferences.
OS X Launch Services may not know about an application while an update is underway - which is possibly what happened in your case.
Best regards,
Felix Schwarz