I seem to recall that Dark Empire
handled Leia's pregnancy with Anakin without acknowledging she'd already had Jacen and Jaina, which led me to believe at the time it was a separate continuity from the Thrawn trilogy. I quit reading it pretty early on though, so I could be wrong.
It seemed to me that later works took the two unconnected stories and then tweaked the timeline to make them both fit.
ETA: But getting back to the original point, I would also like to see the occasional comic that does fit in with the current post-Destiny status quo. But since this new mini is going its own way, I doubt IDW would do that, as they'd probably consider two different post-Nemesis comics to be confusing to the casual reader.