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If you dump it all in the same directory, I can't see how you will ever get it sorted out again even if you are lucky enough for there not to be a duplicate name.
I really don't know anything about vb. Once in a similar situation I dumped all the new files in a directory under the main site. When I was ready to switch over all I had to change was 2 lines in the config file after I copied all the files to the root directory. The ones that specified the base url.
I think I would try that before I broke my main site.
Sorry I can't be more help.
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