That is what i thought.
So i got my memory a little mixed up because i read both originally around the same time. Have not read Dark Empire in over ten years and am afraid it would be too jarring to read again as i think it has probably not aged well. Loved it in the 90's.
I bet i would be super critical of dark empire II and Empire's end as well. Probably better left in memory only.
Also if i am not mistaken Zahn, Veitch and Anderson tried to have some kind of overlapping continuity if not successful in execution they had the idea for the stories to intersect.
Worst thing about the Jedi Academy trilogy for me was Mara and Luke not being together. But apparently that was a decision that came from LFL and they did not relent til vision of the future and union were published.
Throw in Barbara Hambly not being on the same page and creating Callista its sort of a mess.