A Separation Agreement itself can include a provision in terms of how to modify or change the Separation Agreement when both parties agree, so that you do not need to actually have to go to court, but there are downsides as well. For example, the parties can change the Agreement by putting a new provision in writing, and it would require both parties to sign and put up a notary public. However, Judges in Probate and Family Court do not need to accept the revision(s), since it was not presented for the courts approval, and would not actually be a Court Order.
It basically means that the Agreement could be there between the parties, but if someone does not follow the change that was agreed upon by both parties; and it is not part of the court order, it can’t be subject to a contempt action.
There are still some civil court remedies that could occur, but a better practice is to generally file the Modification in court with the Stipulation for Judgment and have the court approve it, if you want it to be legally binding in Probate Court.