Yeah, if you read Outbound Flight
, Thrawn's contact with certain humans was essentially "first contact" outside the Unknown Regions. That is how it was written at the time, at least.
I always like to post Timothy Zahn's response about this:
"Ours is not to reason why..."
If I had to hand-wave this one, I'd probably say that over the thousands of years between SWTOR and HttE the Chiss pulled back to their own territory and the records of them were lost.
From another point of view, of course, the fact that the game designers thought the Chiss popular enough to include is a wonderful compliment. However we have to work things to make the the continuity shake out, it's an honor to have Thrawn's people kicking butt and taking names.
Now if only someone could get them to ask me to write a side adventure ... <G>
I suppose, with everything that did happen in the next 3000 years, that old records could have been lost, purposely destroyed, forgotten. If we accept Chiss in TOR we do just have to accept that.
Knowing how isolationist the Chiss are, I can see them eradicating any information of past alliances (though perhaps the information still exists somewhere). And on the Empire's side, there was a really good post here some time ago that explained pretty well how all that info could have been lost, but alas, I can't find it.