Well Telos also indicates they recognize original X, when Phantom and X go to Levithan and Fefnir.
I feel that the Four Guardians have always consider Copy-X as a ressurection of the original X who put his previous body to rest to seal Dark Elf. From the start to finish, they see him as only one X, the person they will always be loyal toward.
History records X using the "Dark Elf," but whether that actually means post-curse or if it's due to some historical inaccuracy is up for debate;
The Dark Elf is a special type of Cyber-elf created to bring the Maverick Wars to end... X used it and the wars quickly ended... After that, it was stolen by someone, and then the Dark Elf brought about the Elf Wars.ZERO3 says roughly the same thing, until it is revealed that Dark Elf was once Mother Elf. So, it's not so much that X used "Dark Elf", just that they didn't know her other name. As you can see, it clearly says that after she was used by X, she was stolen and cursed. Therefore, X actually used -Mother Elf- to end the Maverick Wars, afterward the Elf Wars happen.
This is different from Zero´s use of her, who we know only appeared in Elf Wars. The "fake bad Reploid's bossing around" of Dark Elf happened in that timeframe. Which is also why Dark Elf knows his name.
further muddling this is the fact that the Elf Wars is by some accounts considered the tail-end of the Maverick Wars and by others considered its own distinct event.
This one´s definitely an issue. Especially when such matters as the Shining Arms, Neo Arcadia´s founding and the Four Guardian´s creation are involved. Originally in ZERO2, X created Neo Arcadia after the Maverick Wars, but as of MMZOCW, this happened after the Elf Wars. Ofcourse, since the latter is after the former, both entries do not contradict.
In regards to Neo Arcadia's creation and Elf Wars, the forests of Anatre, Dysis, Notus and one other, which surround Neo Arcadia east, west, south and north respective seem to be one of the most notable examples of the historical cover up (aside from the sunken library). The ruins are the secret of the Maverick Wars, are part of a lost civilization, forbidden places that were relics build during the old great war time, yet in truth hold many important truths about the Elf Wars. In these place, originally Repliroid research was carried out from a very natural point of view. This places them on similar levels of importance as the forgotten laboratory (historical ruins), the laboratory hidden in a forest in which Zero was sealed and research was likewise carried out.
I feel that those facilities are innately related to Project Elpis, which in turn relates to Neo Arcadia's founding principles. Project Elpis is a step toward Neo Arcadia's creation, to the point that many of the things that were created to be part of Neo Arcadia's founding, precede it in order to bring the utopia into existance.
This applies to the Big4 as well. There is a possibility they were created before Neo Arcadia's official founding to carry out its founding principles, but were unable to carry out their duties until Neo Arcadia's founding was completed with the war finally having ended. As such, before taking their place as Four Guardians and working toward their creation purpose of earth recovery, they were forced to become Hunters that worked toward the creation of their utopia.
As Harpuia says: "I am a warrior born to protect humans." Despite their weapons never being built for combat, they are still Shining Arms, the legendary weapons of the top hunters.
The uncertain overlap of Maverick Wars and Elf Wars connect itself to the root of the cover up; Neo Arcadia's founding principles are nothing by a fake, as it is built upon the many corpses of others, a history steeped in madness they themselves created by trusting that man, Dr. Weil. Therefore, Neo Arcadia attempts to cast away it's own guilt by hiding history and covering up the exact time of its founding.
Harpuia, showing his age and wisdom on the matter sums it all up nicely:
The release of the Dark Elf once resonated with Omega, the Devil Repliroid who plunged the world into terror. When the apparition calling himself Doctor Vile appeared in front of me, I knew that the utopia Neo Arcadia was no more than an illusion created at the end of the bloody battle. But if the friends I spent my life with, fought with, made promises with, the sworn enemies I fought my hardest against, were all a dream... That couldn't be. Otherwise everything in this world would be an illusion. All the power, all the deceit, were now to reveal a history steeped in madness.