Change last book to them trying to merge Stolen Lands with First World while others attempt to stop them. Also, are they evil? If not then they may change their opinion when they learn more of her dark feyishnes.
CAVEAT: I'm assuming you don't particularly want the PCs to pledge themselves to Nyrissa. My comments here are meant to support that assumption - not as absolutes about how the campaign has to be run. With that stated, here goes...
The PCs may think they want to seek her out, but my question would be, how exactly are they planning to do that? I'm assuming you didn't give them too much detail on her.
For the time being, just don't let them uncover anything too specific. Over time, let them find evidence that she keeps sending attacks against them (like all the NPCs with locks of green hair in their possession).
When you get a chance, land a couple of low blows. For example, if you roll an Assassination event, consider having her send someone to kill one of the PC's family members, perhaps leaving a mocking message behind. Even crueller, have one of her lock-of-hair-carrying minions destroy one or more of their most treasured magic items, saying they will not be able to use it against his "queen." If the PCs ever successfully interrogate any of her minions, keep a few rules in mind - these guys don't personally know how to reach her, and their knowledge of her abilities is quite limited.
By the time they learn where she is, as scripted in book 6, they'll know they have a vested interest in stopping her.
They are not evil. The party has been acting strongly lawful neutral. They figure she has the longest legal claim to the lands, and as such, it is rightfully hers.
If they do join with her, who would come against them in the last book?
In this case, I'd assume her plot in book 6 wouldn't be aimed at the PCs' kingdom. So instead, aim it at Pitax, with that nation sending a large team of high level adventurers (Irovetti leading them) against Nyrissa.
Alternately, make the final enemy be Brevoy. This requires more re-writing on your part, but could be a lot more interesting. Assume Nyrissa isn't currently trapped in her realm, just exiled from the Fey Courts. Most of the critters written in book 6 don't work for Nyrissa. Have the events in chapters 4 and 5 proceed as written. Toward the end of book 5, let Have Choral the Conqueror return to Brevoy and be revealed as
and lead the war against the PCs and Nyrissa. Choral can eventually invade Nyrissa's palace, sundering it from the world, and the Blooms are a spontaneous result of that sundering. The PCs have to invade the sundered pocket realm, fight past all the encounters there (which in this version are allied with Choral, not Nyrissa), and rescue their queen from the Conqueror.
Like Cintra says, knowing about her and being able to contact her are 2 entirely different things. Also, she is from the First World, CAN she have any legal claim to the Stolen Lands. But what if they succeed? Then they have become vassals to a fey that is insane, even by First World standards. Play up her obsession and feyness. It should be fairly easy, if they have any decency whatsoever, to turn the pcs against their new liege.
When we first heard her story we felt sorry for her and were thinking how we might help her recover her >you-know-what<. But after everything she does, we knew she had to die.
Remember, she's chaotic, insanely, blithely chaotic. If your PCs do somehow link up with her, she'll still leave a trail of devastation behind her (thus I would leave the events of RRR, VV and BFB pretty much as written.) This might make them begin to question their allegiances.
Once they get closer to Book 5, she should start making more direct appeals and appearances. And that means turn on the fully crazy. And then there's the final reveal, which is Book 6, and if they truly are Lawful, they should realize what a huge mistake the alliance was, and attempt to defeat her.