I would think you would want to do the reset prior to the full re-scan, but that's just my view on it, and I do not know if that would correct your situation or not.
 
Bob Bone

I never mentioned anything other than what you have now done,  You had to re load a fresh kit inside SD 3 and I'm glad I was correct. Please read post # 7. 
And as said above you can share the kits that came with both SD2 and SD 3 , most remain the same anyhow. 
There's nothing broken or wrong. You are just using new software. And it's common to loose little details like VST pre sets when we upgrade. This is normal. I had no problem finding my Yamaha Birch kit and a few special snares I use. 
If your in the habit of not finishing projects and upgrading, expect to have to do a lot more work. 
You can always use Session drummer 2. I still have it as I always install 8.5 to get True Pianos. But you should have installed the older software first. 
 

Yes i want to go through that article Mr Anderton linked for sharing those two SD's.   I'll close off this post now and thank you all very much for your replies and help.  There have been some very good ideas here and I appreciate your time and help guys.   Just in closing Sock, i should note, the songs didn't go funny right after the upgrade.  The songs were opening fine for quite a while now following the upgrade. I'm not great at mixing so these songs did need more work anyway so it's probably not the end of the world.  My main nightmare was the fact that a song which was nicely mixed and ready to go was at risk.  And like i say, i wanted to send that one into TAXI and the deadline was yesterday.  Fortunately, I had already an MP3 made of it so i got the song sent in.
Hopefully, once i replace all the SD2 drums with SD3 going forward I should be ok.  I'll create a custom kit once I pick out a nice snare, kick etc and make a note of where these are saved.  At least then i can simply reload that kit as you do with your Birch kit.    Thnaks guys.  Have a great weekend.