Normally, claim preclusion only bars later assertion of a claim only if (a) the plaintiff could have brought that claim when it filed an earlier suit and (b) the later-asserted claim is the “same” as a claim in the first case (courts take different approaches to how closely related the later claim must be to the first, but the federal rule is to look at whether the later-asserted claim arises out of the same operative facts as the earlier claim). So, normally, if a patent issues to the plaintiff after the first suit is filed, claim preclusion wouldn’t apply because of the first step: you can’t sue for infringement until the patent issues (with the narrow exception of seeking “provisional damages” for infringement under Section 154).
But, in a recent case, a district court held that the plaintiff had a “duty to seek to amend” its complaint to add a later-issued patent, and to the extent the defendant can show that its infringement arose out of the same set of facts as the earlier case, claim preclusion will (and does) apply. The case, XY, LLC v. Trans Ova Genetics, LC (D. Colo. 2018), is here. One of the two patents issued after the complaint had been filed, and a second actually issued after judgment in the first case had been entered! (The district court also took what may prove to be a very unworkable approach to determining the second step.)
So, be careful out there: this creates a real mess because now you’re going to have to assert every possible patent for infringement, and if a new one issues, you better move to amend and hope the judge grants the motion, or doesn’t, because then you’ll be starting all over again with discovery, claim differentiation issues, and so on… If you’re a defendant, maybe you should consider seeking a declaration as to patents the plaintiff owns, but hasn’t asserted, and just make a mess that way.