Here are some theories I have towards how Lion Guard could fit into The Lion King 2 Simba's Pride and the Lion King series as a whole
1) Quite simply they were off on another mission, which is not far fetch'd if you think about it. I mean, its like the Avengers, of which this show is partly inspired by: If the Avengers were responsible for helping out EVERY "big problem", then what would be the point of every other superhero existing in Marvel like the X-men, Spider-Man, SHIELD itself etc.? They specifically can't always help out EVERY problem of course. Besides, the Pride Lands and Africa itself is a HUGE place so they could have just been busy with something else.
2) Possibly, because of Kion's friendship with hyena Jasiri, of which Simba does not currently know about. Maybe its a scenario where when Kion got older there was a misunderstanding with that Jasiri could have done something and Kion had an argument with Simba over it, and Kion just ran away with her because "we are the same", which would further motivate Kiara to prove Kovu's innocence and her independence when she got older
3) Very possibly, like with Simba and Nala's original son Kopa in the Lion King books, Kion went off to form his own Pride, or even Lion Guard somewhere else outside the Pride Lands. Like I said, Africa is a huge continent after all, and the series is said to be set in Kenya, so Kion and the Lion Guard could have moved to another part of Africa. There is also a chance that Bunga could have persuaded them all to "Hakuna Matata" it all when they got older, like his uncles
As you can see, its pretty much common sense as to how it can still tie into the series. They were able to make Megara appear on an episode of Hercules: The Animated Series, which is a midquel series like this and they were still able to make it work without ruining the continuity, so they could find a way to make it work here. As Kovu and the Outsiders are going to appear on the show, it is likely that they will find a way to tie it all in together, perhaps by the series finale if nothing else.