Hi,

is there a way to export a ePub with highlights as pdf from KOReader?
Nope.
Thank you for the answer. I'm trying to find a way to use KOReader half screen on Onyx Boox, to take note on the other side. I can not with KOReader, I was wondering to export to PDF and use it. But as you said, I can't.
If it were to work, it would likely be something the the Onyx software would setup allowing KOReader (or perhaps any reader) to run in one half of the screen and a note taking app (or perhaps any other app) to run in the other half. In any case, KOReader would be only one of the apps the Onyx device would be running. It could be in how they implemented the Android OS.

Luck;
Ken
Pazos talk about this in this thread. It could be done, but it is not easy.