My file loss problem continued today, unfortunately. I did another connect this morning, and checked everything OK via file explorer, disconnected and watched Gallery collect files until it was completed, then discovered there again many directories and files removed.
I reconnected to the PC, did another restore, and after disconnected watched the gallery, as it counted my picture files DOWN, instead of UP, ending with another 2000, or so missing in the end. During the process, I could actually see some picture counts go negative. Very weird.
Prior to upgrading to 2.2, I had installed a copy of the Froyo gallery, which was still present on my DX, so I actually had 2 different Gallery apps installed, and it occurred to me that they may conflict with one another, and perhaps that was the source of the bizarre behavior in the DX recovery. I uninstalled the one ID'd as Gallery version 1.1.30682-desire, and went through the Connect/Restore/Disconnect routine one more time.
This time, with the second Gallery app removed, the DX recovered normally, with all files and directories present and accounted for. I'll keep watching this closely, to make sure my picture and video files and directories don't disappear in the future, and cross my fingers that this really was the problem - time will tell.