The two missions mentioned above are (most likely) the only two you won't be able to complete in a quick run through the main story once, but there are six other missions that can't be completed at 60 FPS. That said, I would still encourage you to play at 60 FPS and switch back as needed, it really does massively improve the game experience:

Operation Breakthrough: The lone document, "On ROK Manalchemy", is incredibly difficult to pick up on 60 FPS. The cursor does not want to target it and even in the short time between the endless combat waves the game seems to not give you the ability to pick it up. I managed to pick it up a single time after a couple hours and half a dozen attempted runs, and when I finally did the mission did not trigger to move me to the final location anyway.

A Fog-Laden Forray: In the first large area after the fog clears, a couple enemies will not spawn that need to be destroyed to continue with the mission.

Escaping the Imperial Capital: After the first Vajra fight, it will escape and not break down a wall it needs to in order for you to proceed.

Covering the Cadets: The game will very often freeze after a few seconds of attempting to destroy one of the first marked mission leaders. It may be possible to destroy the leader very quickly and still finish the mission, but it froze on me before I could destroy it 3-4 times in a row.

Nox Suzaku cannot be fought at 60 FPS, the game will always immediately freeze after setting up the mission.

The boss that gives the ultimate weapons will always choose Ace when the game is set to 60 FPS, preventing any other characters from battling them or getting their ultimate weapons.

Thank you so much, First time I played try this I abandoned the game because of the framerate, now I can play at 60!

Thanks!

Great mod, thanks for the tutorial :)