Does Rap Pro still show "green" in Command Center after removal?

How did you remove Rapture Pro? C3 only tracks activity within the C3, installing, updated and removing programs via Windows is not accurately reflected in C3.

AT
  Melodine now won't work  and my Spectral Pro VST was changed to unregistered.

Not sure what "won't work" means and am unfamiliar with Spectral Pro. A VST reset simply clears the VST inventory out of the registry and attempts to read all the VST plug-ins in the scan path in order to rebuild the inventory. Out of curiosity what OS is this machine running? I know some have reported running some older 32bit plug-ins have had to run the current release of SONAR as administrator when they did not recall doing so in the past. I have not experience the problem though.

How old is this version of Melodyne? Which format is causing the problem, VST2 or VST3?
 
Spectral Machine looks like an older 32bit only plug-in. I suspect you may need to run SONAR as administrator from now own to use it. Older plug-ins sometimes rely on parts of the registry which have been secured in newer versions of Windows. As I mentioned above, some Everett users were reporting, some older plug-ins are now requiring elevated privileges where they might not have need them in the past. You might be able to figure out where to hack the registry to open up the permissions or contact the manufacturer, they may be able to suggest a solution. Might be time to retire the plug-in unless the manufacturer is willing to update it to support a newer 64bit version of Windows without having to resort with registry hacks or other security workarounds.

Which Melodyne format VST3 or VST2? If you having trouble with the VST2 format, remove it. It is unnecessary. SONAR uses the VST3 for Region FX and it also may be used in the FX bin.