From what I understand, the MSI should do an uninstall first automatically. Unfortunately, I don't have any experience with SCUP/SCCM so I don't have much more to add. I suspect you'll find more info with a few Google searches or maybe another admin will reply back.
I assume that you know about the Admin Guide http://www.adobe.com/devnet/flashplayer/articles/flash_player_admin_guide.html
I also do not know much about SCUP; is there a way that you could incorporate the executable uninstaller (http://helpx.adobe.com/flash-player/kb/uninstall-flash-player-windows.html) as a first step of the upgrade process?
Thanks for replying.
I’m thinking I should be able to push a vb script to uninstall the older versions out via SCCM or I could use the uninstaller (if it can be targeted to get rid of one version and leave another).
Either way it shouldn’t be to hard.
The uninstaller will uninstall all installed Flash Player versions.