Hey John,
Did you ever find a solution to this problem? I am having the exact same issue where the MXF files lose connection the the string keeping only the first MXF file on line. Seems to be the same problem you are having.
They work perfectly for a long time and then something happens and they are gone. I have to literally go back and replace the files from the original file which will bring everything back together. Unlinking and relinking is of no help.
Wondering if you ever found a solution.
Any help would be greatly appreciated.
Adam