Reincarnation Unclear Lore

Why is 2b's sword in the bunker, and why is the date of the alien invasion wrong?
this is due to the bird virus corrupting the data, and messing with where things are. The devs have admitted that this was mostly just to give more 2B fanservice. the events portrayed in Automata are still correct.

Why is SINoALICE in reincarnation?
This one doesn't have a clear answer, however there is some explanation. At the end of Sinoalice JP(the other servers had a different ending), the game ends with you basically removing the desires of EVERYONE who exists in that world, effectively turning them all into soulless husks. as this world has no future do to everyone effectively being "dead", the sinoalice branch was sealed off. it being in The Cage is not clearly explained, however the two most likely guesses are that since the Library is now useless it's being used as a storage device for the sealed branches, or they just got trapped in the cage.

Why is Noelle so important?
If you noticed, I put alot of noelle's story stuff in the playlist. this is due to the fact that Noelle is actually a part of the normal nier timeline/world branch. Her plot should be fairly easy to follow, but just in case, this video by I AM CAIM does a VERY good job of explaining it. The devs have also confirmed a change to the official timeline(printed in the nier automata world guide vol 2/Drakengard 10th anniversary box) confirming that the crystal Noelle turned into at the end of her Recollections of Dusk story was found by an android and lead to the development of the dragon weapons, due to Noelle/Elanor's ability to just..... do that.

Whats up with the " 62,462 cycles" mentioned in the final lost archive?
So this is where the series gets a bit..... complicated. essentially, the entire series, Drakennier as I call it, is essentially looping over and over, creating new variations on each loop. this is how we can have things like the original nier gestalt, OG nier replicant, and the replicant remake being canon still, as well as the many, MANY different versions of the stage play. the reason this is happening is because of something called "The Fall Down" which is basically the end of time entirely where all the timelines and branches collapse and fall apart. Accord and her group are essentially keeping watch over these branches and timelines, trying to find the one that works out and prevents The Fall Down, as well as the route that gives humanity a chance to come back. as we see with the ending of Reincarnation, they finally found that route, it just took them 62,492 cycles to do so. A quick note, it is most likely just the nier/drakengard specific timeline that is looping. the Timeline Hina and Yuzuki are from for example is most likely not looping, and functions as normal. the cage just..... can interact with the branches somehow. Probably Accord.


When is Reincarnation set?
not really a big question, but there's still a little bit of confusion. Reincarnation has been confirmed to take place after ending E of Automata.