Continuity is the bane of shared universe stories. Comic creators and fans have long wrestled with the difficulties of maintaining a single ongoing story told by hundreds of different collaborators over a series of decades. DC Comics has used multiple crises to explain why Batman is sometimes a lone creature of the night and sometimes a member of the very public Justice League, before finally embracing Hypertime and insisting that it’s all canon. Under the reign of editor Stan Lee, Marvel adopted the No-Prize, handing out an empty envelope to anyone who could provide a compelling reason for Spider-Man complaining about his empty bank account in one issue and then splurging on a pizza in the next.
At this point, Marvel hasn’t digitally altered these issues to make for a clearer continuity, nor is it clear that they should. Star Wars fans still annoyed at Hayden Christensen being digitally added to Return of the Jedi can tell you that consistency is not necessarily king. And no one would argue that the “no guns” version of E.T. The Extra-Terrestrial is Spielberg’s best move.
In the end, MCU fans may need to do what comic fans have done for years and just make up their own explanations or accept that a good story isn’t necessarily a consistent story.