I think in the database?
Easily exported (3 or 4 methods), but not simple to import.
Actual notebooks of either kind are in .nebo files and can be copied between Sage & Elipsa, or imported to Android / iOS / Windows Nebo, but not vice versa. If the LC is having colour in the notebooks they may not work on Sage or Elipsa, but will likely import to Android / iOS / Windows Nebo.
I imported all my notebooks on Sage and Elipsa to Nebo on the TCL Nxtpaper 11, which is far better for notes.
I've no interest in sync of annotations. I only import as text files via Kobo Utilities and Clipboard. You can use Kobo Utilities to read then write bookmarks and reading positions / status between identical ebook files on different Kobos. I don't know if it does annotations & highlights too. Probably not.
I never used pen to annotate epubs as that's pointless. No export possible, unlike Nebo markup of imported PDFs on Android / iOS / Windows Nebo.
The Kobo version of Nebo is too cut down due to eink. No real time conversion preview.
I've Android eink too and my conclusion is that eink is best for reading novels and only short typed notes to be exported with big highlights are any use.
I'll stick to big highlights, short touch key notes and reading on eink. It's just too poor at anything else. The Nxtpaper 11 and my add-on portable 16″ 2560 x 1440 matt IPS screen are nearly as good as eink. Especially the Nxtpaper 11 (incremented 2.0 version of NxtPaper. TCL actually make screens).
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