Hrm. Well according to this, your entire desktop folder is redirected to D:\Desktop, and it is indeed saying files are missing. So "pretty much always" -- if they're unplugged at any time, unfortunately with the current code, their entries would get zapped for being removed.
But, interesting note on my end, that I should probably verify the drive can be accessed at all, before marking a file as missing! So that's something I'll take a look at.
Sounds like you have a seperate problem with folder portals not resuming properly after hibernate?