I have a similar problem, after Anniv Ed loaded on my new primary hd.
I went to Disk Management and found that Drive D (System) was no longer on my primary, but had been moved to my secondary hd. Now when I restart or shutdown/start, it tells me that a "required device is inaccessible. Insert orig disc and select Repair." That's woeful because:
1. it tells me to choose a "target operating system" but only shows Win 7
2. the advanced option wants to delete all apps I've installed and personalizations.
I temporarily get around this by shutting down...start...ESC...selective boot...select primary drive (it finds it somehow)...enter. That works and returns me to where I was with all intact, I think.
Does anyone know how to resolve this?