VST scanning in Sonar X3

This weekend I installed Melodyne Editor 4 and Komplete 10 Ultimate.  So there was a crap load of new vsts to deal with.  (32 bit, 64 bit, vst3).  I already had 5 scan paths and my dlls and vst3s where spread all over 2 SSD and HDDs.  So I figured I'd clean things up.
 
I created two directories on my SSD - c:\VstPlugins (32bit) and c:\VstPlugins (64bit).  Under those I create directories for each product vendor (including Cakewalk).  Then I copied all the dlls and vst3s to the appropriate directory.  If I had a vst3 and a 64bit vst2, I only brought over the vst3 file.  Then I set the search path in Sonar X3 to point to just those two directories.
 
Now everything is screwed up. 
1) If I look at the paths in plugin manager, they point to old locations where the files no longer exist
2) If I try to do a Reset in Preferences, I always get a dialog saying a VST scan is already running.
3) If I start Sonar with a Blank Project, go to Preferences and delete all VST search paths, then try a reset, I still get the VST scan is already running message.
4) Sonar seems to add c:\program files\Cakewalk\vstplugins to the search path (in Preferences) all by itself.
 
So how do I get Sonar to give up on all knowledge of VST plugins and start over, using only the paths I've supplied?
How can I force the "VST scan is already running" to end?
 
BTW - I'm doing Manual scans with no rescans enabled.
 
Thanks
 

The bundled ProChannel Modules are not in "c:\program files\Cakewalk\vstplugins." The path to the bundled ProChannel modules is silently added to the VST scan path at scan time. In general, scan path maintenance should be performed in Preferences > File > VST Settings. I had an issue with an unwanted path adding during installation and found it in HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software\SONAR\Cakewalk VST\Paths. This is not the part of the registry maintained in Preferences or used by the VST scanner. Somehow the path was added to this registry key. SONAR Installers would pick it up and add it to the regular scan path key in HKCU. I do not know if this is what is happening in this case but is it one place to look.
 
Moving VST2 plug-ins around manually often times works but there are cases where plug-ins have additional config files or registry entries which embed the installation location. These will break when moved by hand.
 
Moving VST3 plug-ins from their default location is not a good idea. Unlike VST2, the VST3 spec provides a recommended installation path. While SONAR can work with VST3 plug-in located in non-spec paths, not all host can.

My own policy has been to delete any 32-bit plugins for which I have 64-bit equivalents, but that's only to prevent my own self-confusion. SONAR itself has no problem arbitrating between them, and if you occasionally insert a 32-bit plugin by accident it's usually no big deal.

Thanks, all, for the information.  I have things cleaned up a bit and Sonar seems much happier.  A manual scan of about 100 VSTs takes very little time.  And I'm now getting the vst3 version of Melodyne Editor 4.  Yeah!!!