I have the same issue in Vegas Pro 9 64 bit. Sometimes when I launch Vegas and it opens the last project automatically it'll tell me the media can't be found and to locate its new position - even though it's in the same place!
I find I have to close and reopen Vegas to get it to work again.
I have something similar, there is no message but some of my media (video) changes to a solid red on the timeline. I have to close down and reopen V9 and all video is back to normal.
9 32bit, haven't lost media, but when switching away, then back to vegas i get random pop's and click's in my audio. not there when rendered, or after opening and closing vegas.....