[FencepostErr1r]

Hello everybody,
I followed the sticky guide on how to let Calibre create shelfs from tags.
This works:
1. Connect Kobo
2. Send already tagged / shelved books to device main memory
3. Disconnect & let the Kobo to it's thing.
4. Huzzah! Shelfs.
5. Move book to another shelf or assign an additional shelf.

This doesn't work (this takes place after the above):
6. Connect Kobo
7. Let Calibre do it's thing
8. Check if changes are reflected in my library - NOPE
9. Disconnect Kobo
10. Dear Lord of the dust bunnies under my bed - the changes on my Kobo have been reverted.

TL;DR:
Is the automatic metadata management supposed to overwrite any changes with the libraries contents, or is this a bug?
Please don't tell me that there is no two-way sync, I might finally pop that aneurysm my Kindle gave me when I found out that I cant manage my shelfs from the Webinterface.

I already tried these things:
- Factory Reset of Kobo
- Double checked the guide mentioned above

Thanks for helping,

-FencepostErr1r