[GeoffR]

Don't edit the books while they are on the device. If the Kobo firmware detects that the book has changed it will be deleted as you have found, but if it fails to detect the change then worse things can happen, as the informatin in the book may no longer match information in the device's database.

Solution is to delete the book from the device, edit the original kept on your computer, then reload the modified book.

Edit: Just to be clear, I mean delete the book using the device's delete function, don't delete it while the device is connected to the computer..