Following up on my comment:
Can't you store the commands you used on your offline db, and then
apply them on the online db, through a script running on SSH for
instance ? Or even better upload a file with all the commands you ran
on your offline base, to your server and then execute them with a cron
job, or a bash script ? (The only requirement would be for your bases
to have the same start point, and same state, when you execute the
script)
I would recommend to store all the queries you execute on your offline base, to do this you have many options, I can think about the following : You can set the profiling level to log all your queries.
(Here is a more detailed thread on the matter: MongoDB logging all queries)
Then you would have to extract then somehow (grep ?), or store them directly in another file on the fly, when they are executed.
For the uploading of the script, it depends on what you would like to use, but i suppose you would need to do it during low usage hours, and you could automate the task with a CRON job, and an SSH tunnel.
I guess it all depends on your constraints (security, downtime, etc..)