Last week, I decided to upgrade my Toshiba Satellite laptop from Mint 17, to Mint 18, which I have on my other machines. It's dual booted with Win 10, as is my desktop. I use Deja Dup for backups on an external drive, and have restored my backups before, with no problems. This time, however, only a handful of backups showed up, while the rest seem to be there, but "ghosted". That's to say, the file names are there, but the text is greyed out, and inaccessible. This, of course, prevents new backups because Deja Dup just backs up new files and changes to old, as I understand it.

I'm not a fan of duplicity - and less so of deja-dup. If I can't get to my data when I need it, it's useless. I've tried duplicity based tools a couple of times and had a devil of a job getting restores to work.

I'm a big believer in basic rsync. I can find my files with any liveCD, and I can easily restore over files as I need.
I can't help with your problem, but I suggest you look at other (better) options.