OK, I got things back (I think/hope) eventually.
I'm on Windows 8.1 and had 30000+ files in quarantine.
I disabled UAC completely.
In batches of about 600-800 a time I asked the files to be rescan-ed (F2). More at a time did not seem possible.
Once they were all done I restored (F3) all files to original location, again in batches. In this case it looks like I could have done them all at once. But I did in batches.
Then I deleted them all from the quarantine directory, in my case C:\ProgramData\Avira\Antivirus\INFECTED
And re-enabled UAC
Mathematica 11 works for me.