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It has only happened twice, and we have undone the deletes no problem, but user is insisting it's not their fault. The biggest problem this could cause is mistrust in the SVN system itself or at least its logs.

They know how to delete files, they use tortoise SVN, and know that ticking a missing file in the commit dialog and commiting results in it being removed, but they insist that this is not the case.

Delete commits are always with changes in other files that are clearly them, so no one is impersonating them.

How can I prove one way or the other it is them or not without holding their hand during each commit?

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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.

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