[Quoth]

I always export notes. Then there is a folder with them that work (text, docx, html, png, pdf). Mostly I export docx from Advanced and png from basic.
Never use pen for epubs, use text as the pen annotations are useless on PC. I think the pen annotations make extra content on a PDF, so you can copy back the pdf. I always read annotations when I finish an epub using Kobo Utilities & copy/paste to a text file.

You can copy the native folders / notes and when copied back after a factory reset, they are re-imported to the database. Probably only the metadata such as names and kind of the notes (basic/advanced) is in the database as I've copied the actual notebook files/foders from one kobo to another and they appear.

A Factory reset will reset & erase most everything.

A logout / login will build a fresh database, but may erase notes folders you created (they can be backed up by file copy). It may erase annotations/highlights/bookmarks.