You probably just want to do a factory reset. This will put the device back to the out-of-the-factory state. The methods are listed on
https://wiki.mobileread.com/wiki/Kob...Aura_Edition_2.
Depending on what the problem actually is, that might be overkill.
If there is a problem with the database, you can sign out of the Kobo account through the settings. This will clear all the Kobo info, but not the sideloaded books. The device will reboot and take you through the setup process.
If you just want to remove a bunch of sideloaded books, you can just delete them when connected to the PC and eject. The device will update the internal database to remove these books.
If you simply delete all the files on the book partition and eject, the device will detect this and take you through the setup.
If you really think there is a problem with the books partition, you can format it and when you eject you will be taken through the setup. But, if this is the case, it is probably better to do a factory reset.