MongoDB Balancer:move data inside replication set or across replication set

Before you go further you need to answer a few questions

• how do you represent files within folders into the database
• how do you represent folders
• do you have relations between folders (parent -> child)
• how often do you expect to create folders and files
• how often do you update existing files into folders and what is the number of files you update

Based on your answers you can have a write optimized schema or a read optimized schema. Write optimized is a schema that contains many entries that are very small or you can use built in operators like $inc over a collection. Read optimized is generally a larger collection like the one you described, into your scenario you could have very easy something like this (assuming all folders are at the same level)

{ "userid" : "email or id",
  [ 
     { "folder1" : [ "file1", "file2"] },  
     { "folder2" : [ "file3", "file4"] },
  ]
}

But with this schema it gets quite complicated if you need to link a folder to a parent folder ... But is obvious that the userid is the shard key.

I guess you mean primary shard is down, because the term primary database is not applicable. The behavior will be the same as losing any other shard. The difference is that both sharded and unsharded collections will get affected.