I’m not sure I’m following what you want to do, so please bear with me.
I’ve just done some testing on this & it seems that if you remove one commission program & add another, then when the next payment is made the entire order reverts to the new commission program. I also tested if this would occur if the product were simply removed from the commission program & it happened then also. This would not occur on any orders that were paid in full, but payment plans go back to the referral partner programs each time a payment was made, so it would look for the highest priority program that partner was a part of (that also included that product) and use that for the entire order. I doubt this is what you are attempting to do, but perhaps someone else can chime in on another solution for you or you could simply realize that it’s not the RP’s fault that the buyer selected a payment plan & simply allow them to get the higher commission on those payments. You would then simply need to remove the links to that program so that no new sales would be registered, but allow the existing plans to finish out.
On your second question, you can add RP’s to a new program and remove them from an old one by using a legacy action set. This action set can be run as a batch on a group of contacts or setup as a part of your campaign.