This is what works for me:
-In Calibre I convert my epubs to mobi using default settings
-I then email or use Send to Kindle to send the mobi file to my Amazon account.
I can then open the book/document on my Kindle PW2 and any of my linked mobile devices using the Kindle app and it syncs to 'furthest page read'.
For me Whispersync doesn't work on any USB loaded -non Amazon books or document
John
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