Both Neo and Trinity were dead at the end, so this one here must be a interquel, somewhere between 1 and 3. and since 2 and 3 are basically a direct continuation of each other, that means it's basically set to be placed between 1 and 2.
I'd guess they wouldn't mess with the trilogy as is, but the fact that there is a significant gap between The Matrix and Reloaded, it could be something they try to fill in, possibly. How do things play out with Tank more specifically, what exactly is the story between Neo and the kid he saves who's obsessed with him, Smiths choice to hide in the system while he plans on how to get back at Neo, a proper introduction to Zion, etc.
There's a lot of unexplained story gaps they could fill in. The problem is do we really care enough since we know how it starts and finishes already based on the existing trilogy?