Do Jahir's prophecies "come true"?

Why yes, yes they do "come true", in the sense that somebody says something very similar. In two of the three cases, they even say it to Lisinthir, just like Jahir did originally. In chronological order, rather than prophesied order:

Only the Open (book 4) chapter 8, the Queen Ransomed says to Vasiht'h:

You will find yourself having to choose, then.

This is aboard the pirate ship, shortly after they're put in the same cell. This is the one that Lisinthir does not get to hear. It's also the one that's least similar to the prophecy - in particular, the "arii" of the prophecy comes from Jahir and Vasiht'h's relationship, rather than being literally echoed in the future.

Still in Only the Open, chapter 14, the Emperor (Kauvac) says to Admiral-East, but with Lisinthir also in the room:

It is not enough to rule. We must also Change.

That's pretty straightforward. Note that this one is said in Chatcaavan, while the previous one was in Universal (that being the only language Vasiht'h speaks).

From Ruins (book 6), chapter 24, Liolesa says to Lisinthir:

The future before us, and the empires we must maintain... only love can hold them. Or the war for them will never end.

Again, the echoing is pretty straightforward. This one is said in Eldren, at a private audience between Lisinthir and his Empress. (Well, as private as an audience with an Empress gets.)