I don't know if there is a best way, Charlotte. But I know there are several ways and some are more logical to some people than other equally successful ways.
Me, I'd load the new gedcom, then enter the unattached daughter-in-law as a 2nd wife of your son, transfer all the children, all the data of his "1st marriage", and all the sources to his new marriage then clear all data from the ancestor-less 1st wife and rename that record "delink", switch to the husband then remove the delink record from your son'srecord, which makes it available for subsequent reuse for another new individual. Or once you've cleared the new and duplicate record of your daughter-in-law, you can just delete it all together if you don't mind number gaps in your database. I've renumbered many a family's database so many times that I've learned that the number sequence doesn't really matter all that much.