After yesterday's 1.0.7 update Keira Metz no longer appears in her house and the marker for her is gone. I had already completed her storyline and used to be able to go back to her at her house as an alchemist merchant.

Is it the 1.0.7 patch that deleted her or is something else going on?

I'm at Level 15 and on my way to Novigrad to find Triss. I hope the introduction of Triss does not delete Keira.

So far as i'm remember if you complete her quest she will went and appear only in the end of the game. So nothing changed.

Not after you completed her storyline you didn't. Once you have done that she leaves for whatever path you took.

Have you really completed her storyline or just the main storyline involving her?
What was the topic in the last dialogue you had with her?

I did her optional storyline including the magic lamp, Fyke Isle visits, favor for a friend, the horse race to the beach scene, the sex scene, the scene where she takes you to her secret private realm, and all that jazz. I was always able to go back to her at her hut and trade with her. But now her marker is gone. I'm reasonably sure she disappeared from my map with the 1.0.7 patch.

You have not completed her storyline. She is not at the hut because she's gone back to Fyke Isle (after the sex scene) to get Alexander's notes. You have to go there to confront her.