A "location" is just a certain-sized chunk of uncompressed markup (source). Converting changes the underlying markup... plain and simple. There is no way (official or otherwise) to "map" location numbers to the actual text rendered by the internal markup. If the reference numbers for the Kindle version are important... then you'll need to use the official Kindle version. They simply can't survive a conversion intact.
(or find a way to overcome the clipping limit without a full conversion)
Last edited by DiapDealer; 01-22-2013 at 04:43 AM.