Superman's inability to cure Mon-El is a Stable Time Loop.Mon-El's origin is that Superman put him in the Phantom Zone because he couldn't cure him in the present. The Legion freed and cured him 1000 years later in the future. When Superman visits the Legion he gets hypnotized to forget the future, to prevent time paradoxes. He also forgets that Mon-El has been released in the future, so he keeps trying to cure him in the present. The guess is that on some subconscious level he remembers that Mon-El gets released in the future, and this subconscious memory prevents him from creating a permanent cure.
Mon-El doesn't actually stay in the Phantom Zone for 1000 years.Just curing him today isn't possible since it changes the future. However, the Legion could visit the present, free him, take him 980-990 years into the future, and put him back in the Phantom Zone a few days before the earlier Legion takes him out. He then tells the Legion "honest, I really was in there for 1000 years, and thanks for the cure". That would get rid of most of the imprisonment without changing the Legion's history. It would require post-hypnotic suggestion for the one or two instances where his remembering 1000 years was relevant to the story (like with Lady Memory).
Most of the Superboy/man-Prime events are wiped out of historyThe reason? Comic Book Time. Earth-Prime is supposed to be our world—and regardless of whether you think it really is, it certainly has comic books published like in our world. This combined with Comic Book Time means that his stories instantly fall out of continuity. For instance, Adventure Comics #4 has a scene where he's trying to find Adventure Comics #5, which hasn't come out yet. Because of Comic Book Time, that scene happened more recently than it was published—which means it happened after Adventure Comics #5 was published—the story is no longer possible. Legion of Three Worlds had him being sent to Earth-Prime where his friends and family were afraid of him because they read the comic books showing what he did. Because of Comic Book Time, those comics now showed what he did years before he did it. This not only makes the scene impossible (unless they suddenly went scrambling for back issues and Superboy-Prime, a Legion fan, neither read Legion of Three Worlds when it came out nor had his friends and family show it to him), it also raises the question of whether he's actually responsible for his own actions, or whether comic book writers cause things to happen to characters in other universes.
The Klordny Festival is a celebration of Miracle MondayIt makes perfect sense—we're never told what the Klordny Festival is celebrating, and Miracle Monday is celebrated without any knowledge of why.
Nobody invented the flight rings. They were brought over from the Threeboot.When Supergirl left the Threeboot, she never returned the flight ring. Lightning Saga mentions that Supergirl (Kara) has a flight ring, and one similar enough to Retroboot ring that it can be detected as a Retroboot ring. The current Supergirl annual has her joining the Legion pretty much according to the Silver Age timeline—before flight rings. Most writers seem to forget that flight rings didn't always exist, but it is taken into account in some modern Paul Levitz stories so it does still seem to be true. Therefore stories which show the Legionnaires always having flight rings are mistakes. If Supergirl had the Threeboot flight ring on her when she was taken to the Retroboot, it would have changed the timeline by showing the Legion flight rings before they had them. Brainiac 5 could then have analyzed the ring and the Legion would have flight rings without having to invent them. Reboot
Apparition's third body was sent to the futureVery simple reasoning: one sent to the past (Phase), one in the present (Apparition), so the other one logically would have gone to the future. If the Reboot ever gets their universe back, except a baby Tinya to be appearing out of nowhere any day now. Threeboot
The Threeboot is not really on Earth-PrimeThe big piece of evidence that it is is that Threeboot Kryptonite is able to harm Superboy of Earth-Prime. However, we previously saw that it was able to harm Supergirl, and she's not from Earth-Prime.