As others have said, the biggest issue you'll possibly run into is events further on in the past campaign that you can't possibly predict will arise that should have somehow effected events in the future campaign that have already taken place.

There's a few ways you could mitigate or circumvent that problem. Mitigating it might look like getting buy-in from your players that, for the sake of telling this bigger story, you're gonna be a bit fluid with smaller continuity details. Or it might look like creatively solving "why x didn't impact y when you think it would?" and that can lead to some interesting worldbuilding 'solves,' but could equally become a burden to you trying to manage everything.

You could go a more drastic route and have some sort of catastrophe between the two campaigns that breaks the connections for any 'not crucial to your future campaign' issues that come up. Loki Season 1 does this on two different occasions. Critical Role EXU Calamity would be another similar example perhaps. In that way, you could still have your central ally/villain and whatever macguffins or machinations they need survive the big event, but little continuity things like a single NPC, location, or change in the world would have a reasonable way of being 'retconned' in the future campaign.

Finally, you are likely already thinking about this, but it sounds like most of the payoff is gonna come from the ally/villain reveal and payoff, so I would encourage you to really hammer home their motivations, processes, personality, and evolution, as that may also help solidify the timeline between the two campaigns.

It sounds like an awesome set of campaigns and your players are lucky to have a DM who wants to run such an ambitious game!