Will the physical height lost in 3D would be same if I descend with 500 fpm from 2000 to 1000 feet compared to descend with 500fpm from 20000 to 19000
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No, the exact physical height loss will not be the same when comparing different altitudes because aircraft altitude is based on pressure altitudes and altimeter settings.
When you add local temperature and pressure differences into the equation, the altitudes will never be exactly 1,000 feet apart. That is one of the reasons why Air Traffic Control uses 2,000 foot separation above 29,000'.