Site deleted by removing Snapshot

Hello everyone,

We used Snapshot plugin to clone a site from "classic" hosting to our Prosites network. It worked fine and everything, but when we tried to remove the Snapshot backup file (as it's obsolete at this point) the theme for this site got destroyed, any idea why? We would like this Snapshot file gone because it's just taking up space and it's not actually doing anything as we do entire network backups, keeping sub site backups has no sense.

How do we move The theme to be managed by the network and the multisite theme manager?