I've never gotten an invalid format error. try this, maybe your just doing something silly.
get your library the way you want it.
plug in your reader. click it and go to the sync page.
check the collections/all library. you want.
wait for it to finish syncing by viewing the status page.
when done close the ebook library or hit the eject button next to the reader in the library, unplug the reader. before unpluging make sure the reader says ready to disconnect, not "DO NOT DISCONNECT!"
it will spin for about 5 seconds, and it will be done and working.
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