We are sorry for the troubles, thanks for letting us know you could resolve the problem!
A single accidentally hidden slot should actually not cause no atlas being assigned. Did you receive any other error description in the Console window upon import (or when re-importing the directory of your skeleton assets)? If not, could you perhaps send us the problematic exported assets, then we can have a look at what exactly is going wrong, and perhaps provide at least a better error description. You can attach it to a forum posting, or send it to contact@esotericsoftware.com.
