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DJI is currently populating the EXIF altitude using the GPS derived numbers. The GPS altitude numbers are notoriously bad.
If you are working with other software you will have to figure out how to rewrite your tags or something.
If you were processing using Maps Made Easy and both flights took off from the same location, we will take care of that and use the embedded relative altitude as read by the barometric altitude.
Read more about it here:
http://support.dronesmadeeasy.com/hc/en-us/community/posts/204995406-Inconsistent-Elevations