Originally Posted by martz
There are several excellent tools for managing annotations on PDF documents. But has someone figured out a way for converting an EPUB file with annotations and highlights to PDF?
I'm afraid part of this request is going to be nearly impossible. EPUB is, like HTML, just a string of text that the viewer is responsible for laying out. (PDF, on the other hand, fully describes the layout of each page.) So to be able to match up the handwritten annotations with the text, you'd have to write a EPUB layout engine that works exactly like the one in your Reader. Don't count on this happening. (Highlighted text doesn't have this problem, but I'm unaware of anyone who's built that part.)
As a work-around, you could convert your EPUB to a PDF before
loading it onto your Reader, and then use something like PRSAnnots
(shameless plug!) to get the annotations you made on the PDF. You'd lose some of the flexibility of the EPUB (changing fonts and the like), but if you make good choices when creating the PDF, you might not care.
As for converting EPUB to PDF: Apparently Calibre has this ability, but I haven't tested it out. Since you're on Linux, you probably have a print-to-PDF functionality, so any ebook software that can print could be used to make a PDF as well.