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Is there an easier way to rotate a project?

Hello! I’ve used Pix4D as a trial to try and generate a 3D “corridor map” of an air conditioning duct I flew my micro drone through. I got some good footage, ran it through Pix4D but the XYZ orientation was wrong.

This was my first attempt:
https://www.youtube.com/watch?v=Dv6eKSLSVco

When I try and change the orientation, I lose my triangular meshes and I can’t get them back. Please see this screenshot:
http://i67.tinypic.com/oa4ydf.jpg