I did this for a migration, I still have the steps handy... You add a "--drop" parameter to the mongorestore. I'll give you all the steps I used.
Mongodump the databases on the old environment:
Change directories to where mongodump resides (/usr/bin)
mongodump --username=sametimeUser --password=thepassword --gzip --db=chatlogging --uri=mongodb://<mongoserverhost>:27017 --authenticationDatabase "admin"
Now dump the meeting database:
mongodump --username=sametimeUser --password=thepassword --gzip --db=meeting --uri=mongodb://<mongoserverhost>:27017 --authenticationDatabase "admin"
Now dump the userinfo database
mongodump --username=sametimeUser --password=thepassword --gzip --db=userinfo --uri=mongodb://<mongoserverhost>:27017 --authenticationDatabase "admin"
change directories to dump (/usr/bin/dump)
zip the contents:
tar -cvzf mongodbs.tar.gz *
Copy your zipped file over to the new mongo server.
Make necessary ownership/permissions changes so that you can extract the file as yourself.
take the zipped tar file from the mongodump and extract it to /tmp
The result should be a folder for each database under /tmp, like /tmp/chatlogging and /tmp/meeting
Issue the mongorestore command for chatlogging:
mongorestore --uri=mongodb://newmongo:27017 --username=stadmin --password=thepassword --db=meeting /tmp/chatlogging --gzip --drop --authenticationDatabase=admin
Issue the restore command for meetings:
mongorestore --uri=mongodb://newmongo:27017 --username=stadmin --password=thepassword --db=meeting /tmp/meeting --gzip --drop --authenticationDatabase=admin
Issue the restore for userinfo:
mongorestore --uri=mongodb://newmongo:27017 --username=stadmin --password=thepassword --db=meeting /tmp/userinfo --gzip --drop --authenticationDatabase=admin