The Kindle's flash storage is actually divided into multiple partitions. The only partition visible via USB is a FAT32 partition mounted to
/mnt/us/.
Collections data for sideloaded books are stored in
/var/local/cc.db (iirc) which is inaccessible to us unless the device is jailbroken or have serial port/hardware access.
Two options if you want to be able to restore collections:
- Send/email books to Kindle so you can make use of Amazon cloud syncing
- Jailbreak and use Calibre + Kindle Collections plugin + LibrarianSync (JB may not be possible depending on model and firmware version)