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In that case it is likely there is some other proprietary bit in the azw3 file that needs to be set -- unfortunately the only way to figure that out is via reverse engineering and I dont have the time for it right now.
If you are technically inclined you can dump the contents of the azw3 file using
calibre-debug file.azw3
do it for the before and after files and see if you can spot any significant differences
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