Unfortunately, this doesn’t apply to just virtual folders, but all folders under an IIS web server, as I found out a few years ago when I backed up a site that I knew would be taken down very soon (ironically, because the company [SysInternals] was being taken over by Microsoft) and mirrored it on my Home Server, which runs IIS.
The solution I used was to add a character (in my case an underscore “_”) to the end of all the directory names ending in “.com” and then doing a global regular expression replace through all files in the mirror to replace any occurrences of these directories.
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