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Greetings from a distance, I regret that you have problems in the transformation of coordinates, I do not have much knowledge in the program, but I could suggest the following:
If you already have all your project generated in UTM / WGS 84, I would recommend that you export all the information with the initial coordinate system, and those files exported with a third program transform it to the desired system, I imagine that there would be no problem with the elevations wrong ...
Another option would be that at the beginning when you create your project, insert the images and control points, do first hand the transformation of coordinates and after that all the processing with AGISOFT, I imagine that with it the processing would be done with the new system of coordinates and when exporting the information in the end you would not have any problem ...
That's my little comment, if I'm wrong, I'd really appreciate it if you could correct me ...
And if you have already solved the problem, it would be good if you could share how you did it ...
You have a good day...
Atte.