Well, I did not mean multitasking in joined documents into one. I meant that if one wants maintain the integrity of links for several documents, solution would be to join them into one. And at the end join this joined file with clippings and notes into one pdf file.
One would have all resources at hand with working interlinks between actual text and clippings.
My long desired feature is the export of pages or even better sections of pages with scriblings. One could make notes to text and at the end pdf "extract" would be created. It seems to me really cool and easy to implement. A big book might shrink into several pages of interest.