What are possible drawbacks of an IIS 7 site having an NTFS junction as a web root?

a way to deploy ASP.NET code with as little site disturbance as possible.

It seems like this objective and your proposed solution are not aligned, because you now have a bunch of extra work or scripts involved for every deployment.

One thing I have seen is to install an svn client on the production server, and the production site is a checked-out copy of a specific location/branch on the source control tree. This way at least you only have to update changed files for new deployments.

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