Apparent solution: upgrade to Retrospect 6 - it sees the files again, but then I have been getting Assert Error 1582 on starting the backup. Looking at the Dantz Knowledgebase, it says to patch Retrospect with their driver upgrade for Retrospect 6 - Driver Update 5.4.104. Turns out there is some issue with having more than 2 gigs of RAM and Retrospect.

I'll be patching soon, and will post the results.
I need to backup my PC drive, so I hope it works!