@jangell2: The ones that have extra stuff in the sidecar directories are the one you read (or at least opened once).
Did you change the directory structure Calibre uses when sending books at one point?
In any case, Amazon downloads book straight to the documents directory, while by default, Calibre doesn't send them there, it puts them in some kind of hierarchical and organized directory structure (can't remember the defaults, but probably based around Last Name/First Name of the author).
That (and the terrible default Amazon filenames) should tell you which is which
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