I'm sure that discussions have been ongoing, and that things will fall into place after the Tonys. If I'm one of the actors nominated for a Tony, I would absolutely hold off on making a commitment until I find out whether I get the Tony (and can leverage that into a nice hefty raise if I do agree to stay). I also suspect that the producers want to hold off on making any announcements about OBC departures until after they benefit from the inevitable bump in sales after Hamilton cleans up at the Tonys.
As for Lin, I suppose it ain't over until he tweets it's over. But all signs point to him leaving whenever his contract is up in mid-July. He's basically said as much in the RS article, and previews started last July 13. So ending on Sat Jul 9 makes a lot of sense. That way, he can have a big sendoff then and his replacement can start afresh the following week.
And seriously, if you're Lin, why would you stay? The royalties are rolling in, so he doesn't need the money. And he seems to have lots of projects and perhaps even a new musical in the works. Also, he looks exhausted and probably would like to have a little more free time to spend with his family. (I also bet he can't wait to cut his hair!) For those of you who will likely miss him performing in Hamilton on Broadway, keep your fingers crossed that some of the other great members of the OBC stick around ... and keep in mind that there's a decent chance that Lin puts on his breeches again for one of the touring productions and/or in London.