You can put them back right after you do the update, if that will make you feel better, you just remove them from the trash--they stay there for 30 days.
There is also a new option to remove books directly from the Kobo reader. When you are in "books", look at the menu. Delete book is one of the choices now. This doesn't btw, remove the files you may have loaded via Calibre--just the Db connection, so for removing Calibre books, your best option is still to do that from within Calibre.
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