MCU Film Theory: Nick Fury Has Been An Alien ALL ALONG
In order to understand when Fury was replaced by Talos, you have to wonder also about when he came back into contact with the Skrull and why. If the race were heading out into space to find their own new planet and the rest of their people, why would they be back in a close alliance with Nick Fury and Earth in the 2020s? Without the Kree to worry about - thanks to the Peace Treaty signed in Guardians Of The Galaxy's timeline and Ronan's death - they should have been in their new home. Presumably feeling particularly safe thanks to their relationship with Captain Marvel.
So what gives?
Could it be that Captain Marvel abandoned the Skrull soon after leading them triumphantly into space in 1995? It doesn't sound particularly heroic, but there's a hint in Avengers: Endgame that can easily help establish why that might be the case. As a Kree warrior, Danvers' entire existence is geared towards hunting Skrulls for the protection of her people. It was her Prime Directive, essentially. When she learned of Talos' true tragic story, she appointed herself the protector of the Skrull people, but by the time we find her in Endgame again, she announces herself as the protector of multiple planets and multiple worlds.
That's the given reason that she's off-planet for most of Endgame's run-time. She has other priorities that are amplified by those other people not having their own Avengers. So at some point, Carol has to have come to know those races and their vulnerabilities. She has to have decided to protect them too, which means that she would have to spread herself thinner than simply being the Skrulls' protector, just as she couldn't only look after Earth in Endgame.
Without Marvel, at some point, the Skrull headed back to Earth rather than finding their own planet. Or they were called back...?
Anyway, that still doesn't answer when Fury was replaced though. So let's go through that a little more...