HELP: managing multiple virtual folders of cloned websites

I am an ASP web developer developing a website.

I've got ASP files in many sub-folders of many levels deep.

I've always used:

The VIRTUALSITE name is really the virtual directory created under IIS.

I clone my website multiple times, to cater for different people. So, each person gets a different VIRTUALSITE name.

This gets messy when I need to update the websites. I can't do a diff/merge because the files of each site had a "search & replace" applied to them to change the VIRTUALSITE name to the corresponding person.

Has anyone experienced this problem? Can someone give me some tips/solution on how to resolve this?

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