Hi - just wondering if there has been any update to Calibre to fix this issue.
Had the same problem - updated to 3.0.1 on my ipad - all my sideload syncying broke (although it still worked fine between PC and Kindle).
Editting the asin with MobiMetaEditorV0.14 to match the Bxxxxxxxxxx in the URL on the kindle website and sideloading to /private/var/mobile/Applications/xxxx/Documents worked (note need to change owner to mobile from root if you use winscp like i do).
Tweaking all the ASIN's seems a bit cumbersome - is there another utility available that can automate that a bit?
PS - I logged a bug report on this to Calibre here - was responded as a "Will Not Fix" by the dev