using snapshot to migrate to multisite install

I have 35 individual sites that I am migrating to another server and putting them on a multisite install. I have used snapshot plugin to successfully migrate several sites already. I have run into a problem twice now that the restore creates an additional uploads folder which does not include the media (pictures) yet the site is looking for the media in that path.

The path for example:

The actual media is restored to the sites/3 folder but the database (or the site) is looking for the media in the second sites/3

The first time this happened I only had about 20 pics in the uploads folder so I just copied them into the second folder that was created and the site works fine. That was a work-around, but did not correct the issue.

This time I have a really big site with a big uploads folder (many years and months) and don't want to recreate it on the second folder system it created.

I'm hoping you can help me.