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I've considered the option to sync a blank PDF or one with a "template" on it. I gave up once I faced a problem with document notes, not notes on notebook, not being saved to the files once you leave the viewer.
I've lost a few hours of studying taking not on a PDF because of that. I was able to reproduce to many files so I reported to Kobo.
This is easy to reproduce if you want to make sure your firmware works: set your kobo to turn off automatically, open a pdf, take note, leave the viewer open with you pdf. After it is turned off, turn it on and your notes won't be in the PDF.
If you remember to close the PDF once you are done, you are good to go.
As for notebooks backup, I used to do like Cootey. Now days I just don't trust the device to store my notebooks so I just use it for draft notes.
I have a strong opinion on what the note taking is for Kobo, but... that would be a rant, not some suggestion.
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