Dragon Pact

There is some considerable disagreement as to the details.

What Dragon 100 says about the staff is almost identical to the description of the scepter in the Planar Handbook: The scepter of Ephelomon grants the bearer total control over red dragons. It allows the user to dominate any red dragons in the vicinity, and allows the bearer to summon and control a very old red dragon once per week, similar to the gate spell. The Planar HB states that If the scepter is destroyed, the pact between the githyanki and the red dragons dissolves. The red dragons do not immediately turn against the githyanki, but only the most subservient ones continue to serve or assist the githyanki in any way. So, strictly speaking, the 3E Planar Handbook is trumping the 2E description.

As to exactly why this changed, I can't say.

The module about the Lich-Queen does not technically affect the rest of the D&D universe (and in fact, it's not even guaranteed that the module results in her being destroyed). However, it is interesting to speculate as to what would happen if she were gone, since githyanki society is entirely focussed on and built around one thing -- her. And, in this case, it is also interesting to speculate as to whether the staff might have been broken as a step towards destroying Vlaakith, because losing these powerful allies at a key moment could easily have been a crushing blow for those trying to defeat her.

Now, you're absolutely correct that the 2E materials say that red dragons have an "eternal" pact with the githyanki. However, another often-neglected aspect of the situation in 1E/2E is that red dragons only assist the githyanki when the githyanki are on the Prime Material Plane. (Fiend Folio, Guide to the Astral Plane, Monstrous Compendium). The Guide to the Astral plane specifically mentions that red dragons are only available as mounts on the Prime, forcing knights to use other mounts when not on the Prime.

The 3E descriptions of githyanki (MM, MOTP, Psi HB) drops this restriction, which in my mind is a good idea. Some things in the 1E/2E material are more interesting when revised, and perhaps the "eternal" nature of the red dragon pact is another one of those things.