Thinking more on this I think that you have touched on the source of the file (a temporary backup from an MS Office program - I have excel, word and powerpoint examples). If I try to delete a file using unlink with the application still open it complains (Permission denied).
The code snippet is from a file replication utility. I think what has happened is that an oen file has been replicated, the original destroyed by the creating application, and then replaced by a subsequent replication event.
The preventative cure is to prohibit the copy of a file with the pattern "/~$" in its path/name. The curative solution may be to delete any directory containing files with this pattern - and recreate what I want from a backup