[meeera]

Honestly, I think the factory reset is the next step. Can I ask what hassle you're trying to avoid? If you've got all your books set up through Kobo, they'll sync, and it will just take time (set and forget time, not your time).

If you've got your books set up through Calibre, just make sure you've tagged the ones you want on the device (connect, look at the books on the device, and give them a tag of your choice), and it's pretty trivial to put them back on, again, just taking a little time (not your time, Calibre's time).

If you've organised your shelves on your device and nowhere else, with sideloaded epubs - get thee to the pinned post on organising your shelves with Calibre. This takes time to set up, but it's worth it.

If it's losing annotations and page last read, use KoboUtilities to save them to Calibre.

I suspect it will save you hassle in the long run, rather than avoiding it - and if you contact Kobo Help, they're going to suggest it anyhow.