So~, a user commits file deletion together with other valid changes and then claims that the file has been removed on his filesystem by some magic and invisible force?
I see two options here: it's either user removes the file or some other application interferes and silently removes the file. svn delete
can't happen by itself as well as a file can't be magically removed on filesystem.
If the situation is recurring, I'd suggest to double-check whether any antivirus or other application silently removes files from user's working copy.
AFAIU you've already checked svn log
and VisualSVN Server logs. If the log entry tells that the file had been deleted from a working copy and the deletion got committed, it really happened and it's the user who committed these changes.
Some kind of client-side logging should help you to investigate this behavior. For example, you can set client-side TortoiseSVN pre-commit hook script to log which files are going to be committed on each commit attempt.