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Let's see if I can really help... I loaded the app onto my MacBook to see what has changed since I used to have a Sony.
First, the view. When the app opens / starts it is in a smaller window that does go behind the dock. If you click on the green button in the upper left hand corner (red to close, yellow to minimize, green shrinks / expands) it should expand into a not quite full screen mode that keeps the bottom of the Sony screen just above the top of the dock. Turn the hiding off before you open the app to test this and see if it works for you the same as it did for me.
To find your missing books… First question, are all of your books epub? If yes, go into the finder and type .epub into the search field and make sure you have THIS MAC selected as the place to search. If they weren't all epub, look by the file type .pdf. I'm unaware of any other file type you could read on a Sony reader, but if they were something different, just look for the file type.
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