If you are using calibre to sideload the books, are you using it for collection management? If so, that should happen automatically as you get the books on the device. If you are not using it for collection management, there is a way to fetch the collections from the device to a column in calibre. Which needs calibre to still be able to connect to the device.
Reloading the device is also something I don't like because of the "Recent" sort. It is based on when the book was added and then the title within the batch. But, the Kobo Utilities plugin can set one of the date used by this (the other is the last read timestamp). I generally set it to the "Date" column in calibre as that is when the book was first added to the library. And will be reasonably close to when I first put it on the device. It isn't quite so good for books downloaded with FFF, as that will update the date when you update the book. But, the plugin can use any date column in the library.
You can keep going as you are. But, I would expect this to get worse, not better. If it is working, at the least you can do some preparation and maybe choose when you do it, rather than get forced into it. And if it is more serious that it currently appears, it will be seen if you restart the device. That will mean the database is reread, and if there were problems writing it, then you may end up with old data.
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