Mongorestore don't know what to do with file "db/collection.bson", skipping

It seems one must also specify -d in 3.0 like this:

mongorestore -d db db

This answer isn't directly related to your issue case, but the same error output you will receive trying to restore mongo data, dumped with --archive option, available since MongoDB 3.2 version. To resolve this you need to specify --gzip parameter in your mongorestore command. Example:

mongorestore -d destination_db --gzip /path/to/source/db

If you have lost your mongoDb just try running this command:

mongorestore -d destination-db --gzip source-db

Where:

• destination-db is the name of the destination database
• source-db is the name of the source database.