I tried FileAssassin but not AdAware.
I'm now thinking it might be something to do with 'copy-on-write'. Today I saw an error message explaining that I couldn't delete a file as it was being copied. When I found out more, copy-on-write is an OS technique for safely copying files that are open. Shadowing may use this technique. It could be that the file I couldn't delete, and finally removed through Unix, was locked for 'copy-on-write' when there was a system crash. For some reason, the 'copy-on-write' flag couldn't be removed.
It's a guess but it's the kind of explanation that works. The fact that the file was malware is, I think, mis-direction.
Thanks for the suggestion.