If you select "Remove matching books from device" you should get a window where you can see which books are selected, where they are located on the device (main memory or SD card) and you need to confirm once again. This should only delete the book from the device.
Also, if you select "Remove selected books" you are asked to choose where you want these books to be deleted, Library, Device or both.
Do you also get these pop-up menus? I wouldn't know any option to change that.
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