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Can you markup sideloaded epubs or kepubs that were not bought from Kobo?
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Only sync is affected by bought vs sideload.
Pen is for PDFs and Notebooks.
It's madness with epub or kepub. Better to use the touch keyboard and text.
Only Advanced Notebook converts pen to text and shapes.
PDFs can simply be copied back to computer.
I've done maybe nearly 1000 docx conversions to epub (only used kepub till I discovered it existed) and read back the text annotations with calibre for a text editor open beside original document (switched from Word to LO Writer about 2014 or 2015 entirely). I used to use "tabbed" Notebook++ editor for copied back annotations but a while after switching to Linux I switched to KATE, which is nearly identical.
The only difference for Kobo with bought vs Sideloaded seems to be Sync.
Madness using images / png annotation with epubs, but you can if you want to.
The kepub is proprietary to Kobo. I prefer to use epub, as that's what is sent to Amazon, Google, Apple, B&N, Kobo, Smashwords etc. Also epub rather than kepub for my 3 non-kobo ereaders that are not Kindles. Apps on Android are epub, not kepub.
But for the three or four methods of export text annotations (or Pen) from Kobo, the kepub vs epub vs sideloaded vs bought makes no difference. Pen is fine to mark-up layout errors on PDFs for POD, or stuff on instruction /manual PDFs. Makes no sense for epub/kepub for export to computer and part of edit / proof / annotate / edit workflow cycle.