Which firmware revision is your Clara HD running? What version of calibre? Nightmode is an older add-on and not really needed with newer firmware. Your collections will not be affected nor will the books transferred to the reader unless you are updating from an antique firmware revision.
Newer Kobo firmware supports Dark Mode though your Clara HD will need to use NickelMenu to enable/disable it, The same for Inverted mode. Dark mode is strictly for reading and does not invert images but does require a reboot. Invert is like night mode and inverts everything though it does take a reboot to enable/disable (the NickelMenu entry does this automatically).
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