This is tested using POSIX environment, especially linux mint. No guarantee will work with others. This technique is using mongodump and mongorestore commands.

Backup From Atlas

Using Atlas
go to specific folder and dump the db.

mongodump --uri="mongodb+srv://<USERNAME>:<PASSWORD>@<CLUSTER_NAME>.mongodb.net/<DB_NAME>

it will create folder dump with collection name inside.

Restore To Atlas

within the same folder, run:

mongorestore --uri="mongodb+srv://<USERNAME>:<PASSWORD>@<CLUSTER_NAME>.mongodb.net/<TARGET_DB_NAME>" ./dump/<DB_FOLDER>/

done.