First they will decide the structure of the sales force. For example will there continue to be a MCR, MCL, CVAS, etc. or will they be combined in some way. Then they will decide on the overall size of the sales force or sales forces, based on how big a territory they project each rep to cover.
Then it will come down to the local level with territory lines being drawn. The most important factors in who stays and who goes will be ranking and geography. They will seek to keep as many top ranked people as possible, regardless of current sales force. They are not going to let an entire sales force, like CNS, go. They will not keep a low ranked MCR rep at the expense of letting a high ranked CNS rep go. They will decide it makes better business sense to retrain the higher ranked rep. The low ranked rep is ranked low for a reason (yeah, yeah, I know, your DSM doesn't like you. Tough luck).
Next they will match up the people they want to keep with the geography they have to cover. If you are a top ranked rep currently covering a territory that will be there in the new alignment, you're all set. If you are a top ranked rep in a territiory with a low ranked rep, the top ranked rep will stay. If you are in a territory with another top ranked rep, they will seek to move one of you to another nearby territory that has a low ranked rep, or to another TA with a territory with a low ranked rep.
As you can see, it all comes down to rankings. Sorry to break the news, but in this game somebody has been keeping score and you don't get a trophy just for participating.