Moving files from a stand-alone site to a multisite network


I just moved a site into my network and it worked quite well using your Snapshot plugin.

BUT, I'm having a problem with some downloadable files. Here's why:

The site I moved is which happens to be the primary domain for my Bluehost hosting account.

I created a new site on my Multisite network and then just pointed the domain using an A record (i.e. domain mapping).

This caused a problem because files that were stored in my hosting account used to have a path such as

BUT, now since the domain is pointing elsewhere, all of those files have broken paths.

I downloaded the folder that contains all of these files but I don't know where to put it in my multisite so that all of the paths are restored. There are hundreds of files, so finding all the download links and restructuring them would take a LONG time.

Is there a way that I can upload these into my multisite so that the paths still work?

Thank you!