You state that the files are on the HDD, but are they in exactly the same place, as when they were Imported, and with the same exact name, as when Imported?
Yes everything has been on the drive and the files were there yesterday. I think I found what the MC1 or MC2 is. I did a multicam sequence as well with this other sequence. I believe I copy and pasted from the multicam sequence to my new sequence a few of these files. Hmmm. But how would that expain this. I did go back to my multicam sequence and it is missing the same parts as well but I can go to the original files and drag and drop them back into place just fine so they are on the drive but miss located by Premier project file? I did do an update yesterday from adobe for premier and it knocked my gtx 560ti card out of mercury so I had to redo the unlock today.
Are you using AVCHD media?
mov. dslr footage