We mostly successfully recovered a snapshot from a dev site into a WP Multisite, however, rather than setting the WP Uploads folder and putting things into the proper subsite's upload folder, it decided to put things directly into /wp-content/uploads. It also didn't change a lot of names.
Originally, the site was part of this WP Multisite install, we copied it out into a standalone install dev site for development/redesign. (URLs changed for privacy) The site was originstall.thecamplamp.com (mapped as publicsite.com using WPMUDEV Domain Mapping) and moved to a single install devsite.wpengine.com
The original multisite install has been around for a while and has the directory structure /wp-content/blogs.dir/ID#/files/ for the sites media, etc.
Upon completion of development, we created a new site on the original WP Multisite install called newinstall.thecamplamp.com, then used Snapshot Pro to transfer the data onto this new install. Upon loading the new install, we found many broken images, and realized that nothing was put in /wp-content/blogs.dir/ID#/files/ but was all transfered to /wp-content/uploads on the multisite. I also noticed that the WP Uploads folder setting was left blank.
Upon manually copying all the files into the correct blogs.dir folder, we found that many images now worked, however, there were still lots of images references to originstall.thecamplamp.com and a few references to devsite.wpengine.com, as well, there were references to /wp-content/uploads which weren't mapped to /files. All of these references appeared in the database in one way or another (and we fixed manually using other tools). We did not find any problems with references in CSS files.
Meanwhile, everything is now fixed, however, I'd like to know someone is looking into this to avoid future problems, as I intend to use Snapshot Pro in the future for similar such migrations.