I'd like to see some things from the Zahn trilogy be true (and wasn't it rumored that Lucas had Zahn write the Specter of the Past/Vision of the Future duology to bring the EU back to some of the basics -- like a "correction" of the EU? And in those two books, the Yoda thing is mentioned again.)

But differences can debunk, but it can also be done in such a way where an explanation will exist. Like if Clones are stormtroopers (and Luke didn't feel anything different about stormtroopers like he did with the clone warriors in Zahn't trilogy) then it can be explained that Thrawn's cloning techniques were not as perfected as Palpatines...

It was the clones of the Jedi that turned insane, wasn't it, like Joruus C'boath? This could be incorporated into the trilogy, and be an explanation as to why the Jedi come up with a way to disappear on death. (I know, I brought this up before.)

But I think you're right. It will either incorporate or debunk. Just because it might be awkward to try to not do either.