Depending upon your hosting company there is normally a process for doing what you are asking.
What you want to do first before you make any changes be certain to perform a full backup of your site. This is critical in the event that something goes awry while you are doing the transfers.
I have looked at a few of the bigger hosting providers and most have a tool in the cPanel for doing this and list of instructions that need to be followed for getting it done correctly.
All of them agreed one thing as I was reading through some of the plans. DO NOT change any of the folder structures of the sub-domains while this is in process. This must have something to do with the public access file that they store pointing to those sub-domains, if I had to guess, that is merely a guess though.
I would check with your hosting provider. My guess is, based on what I have been reading, this is not that uncommon, although I must admit, with supporting over 100 sites, I have never done it, or had a customer ask me to do it.
I hope this helps.