I found a bit of background lore in a late 2e book called Vortex of Madness that shines a light on how most Githyanki learned that Gith is gone and they have a queen now. In a nutshell, Gith, her advisor Vlaakith and probably a host of guards went to Baator to negotiate with Tiamat. Next thing the Githyanki heard about it was the red great wyrm Ephemelon appearing in Astral Space, announcing an eternal pact between Githyanki and Red Dragons, and that Gith would "not be returning". Instead he made Vlaakith I. queen. The adventure "Citadel of Gith Reborn" also deals with the concept of noble Gith-bloodlines that may express greater powers as one of the Githyanki characters who may or may not be related to Gith is being plagued by dreams from the early days of Gith and begins manifesting potent powers that "came unbidden to her".
The same book, set ca. 1371DR, states that Vlaakith CLVII. has been ruling the Githyanki for the past 1,000 years.
