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or is the Calibre metadata stored in the exth record fields?
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Only if you do a mobi to mobi conversion. Otherwise, the original exth records are retained and Calibre's metadata is stored in the external db. So if you just strip and import... I'd think highlights (facebook/twitter) would show up correctly and the book
SHOULD sync -- don't quote me.
As for an ebook purchased from another site, I can't see Amazon checking
all of the exth records for a complete match. More likely, if the ASIN (record type 113) exists and contains a valid Amazon ASIN -- and the cdetype (record type 501) exists and contains 'EBOK', then things might (just might) work as expected.
Exth record types 1, 2 and 3 may also come into play. If I get a chance to play around with it today, I'll see what I come up with.