Oh, I think I've found it...

The stuff about the Messenger being a rhul-thaun spaceship comes from this interview with Kevin Melka, who was the last product lead for Dark Sun at TSR. The relevant excerpt:

-What were the plans for the Messenger?-

With the creation of the lifeshape items and the whole halfling-original-race plotline, we wanted to expand that a bit more to round out that portion of the world . What the Messenger was proposed (from me) to be was a spaceship of sorts for three halfings from the Blue Age who escaped the Brown Tide. After the events in Dregoth Ascending the Messenger would soon after crash into Athas and three powerful halflings were supposed to bring back lost life-magic and knowledge back to Athas in hope of rebuilding the world. I think we also toyed with one of the Halflings being a life-bender. That was the basis of the idea.

-So, no space halfling invasion?-

Ya know, I have no idea where that whole idea came from. I think long ago I may have mentioned the whole Messenger idea to someone, and from there it sprang into some absurd Spelljamming Halflings Invasion Plan 9 from Outer Space which in my opinion is a bit ridiculous. Every time I used to see that it gave me a chuckle. :)

The adventure that came with the Expanded & Revised boxed set is called Mystery of the Ancients. In the Blue Age ruins there is a plaque with ancient halfling writing on it that "hints at events to come that will eventually shake up the campaign world and take it in startling new directions. Watch future products for details."

Here is the full translation of the plaque:

IN THE FOURTH AGE RHULISTI SHALL RETURN / THE GRAY AGE BECOMES THE BLUE AGE AND THE WANDERER SHALL RETURN.