Does delaying the re-performance of Fajr prayer after invalidating the intention for it until after Jumu'ah prayer count as intentionally abandoning the prayer?

The prayer becomes invalid by nullifying one's intention during it, or by hesitating to nullify it, because the continuity of intention is a condition. If you were aware of this and did not repeat the prayer, then you intentionally abandoned it, and you must repent for that. We advise you to avoid obsessive doubts regarding the intention.