MongoDB - Change primary shard only for a certain database
Yes you can with a single command: 

db.adminCommand({ movePrimary : "YourDBName", to : "shard001" })

then is important to flush configuration on all mongos (suppose all than the one that did the move, but better be safe):

db.adminCommand({flushRouterConfig: 1})

If your databases are small you can do it on-the-fly, else you better plan for a downtime only for this database during the move process. 

Useful link:
http://docs.mongodb.org/manual/reference/command/movePrimary/