If you load all books via calibre then it's really easy to reset and reload. One method would be to use the reading list plugin and add all books currently on the Kobo to a list. With the device plugged in, sort the library view by the on device column and then add all those books to a to reload list.
The other approach is just to plug the Kobo in and do an copy of the directory tree, and then after the reset copying all back.
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