As I understand it, it's legally very hard to strip someone of citizenship, even in this kind of scenario. Not to mention it would be a very bad look! Most serious proposals for a transition to independence (this stuff has actually been discussed!) include, not just Puerto Ricans at the time of the split retaining their citizenship, but the possibility of dual citizenship, etc. Of course, all of this would have to be negotiated. But I think it's a reasonable assumption that it would be to the U.S. and PR's mutual benefit to come to an arrangement that is not unnecessarily disruptive and punitive.
Would some still leave? Sure. But many who prefer to live in the U.S. already do, and have done so for decades. Also, a dirty little secret of Puerto Rican politics is that many if not most pro-statehooders, who would in theory be most upset about losing citizenship, are among the least well-positioned-- from an English-language proficiency standpoint and otherwise--to just pack up and move to the States.