Hi John. Im not sure what your intended workflow is. I will provide you with an overview of the three main coordinate systems used in Pix4D to see if that helps clarify the issue. You should not be changing the image coordinate system in most cases. This is likely the reason that you are having issues. The 3 coordinate systems are the following.
Image Coordinate System: This is the coordinate system in which your images were acquired in. Your drone is equipped with a GPS system. Whenever your drone takes a photo, it writes positional information to the metadata of your image (.tif or .jpg). This positional information is known as a geotag. Geotags are acquired and marked in the coordinate system in which your drone’s positional system operates on. Most drones geotag their images in WGS 84. Your image’s geoinformation is retrieved and extracted from the EXIF data after you import our images into Pix4D. It is best practice to never change your image coordinate system.
Output Coordinate System : Your output coordinate system is selected when you initially set up your project. This is the coordinate system in which all of your output files and products will be in. You can learn more about changing your output coordinate system by reading HERE. Your output coordinate system can be different than your image and GCP coordinate system, Pix4D will go through and complete the appropriate transformations.
GCP Coordinate System: This is the coordinate system in which your ground control points (GCPs) were acquired in. You select this coordinate system when you import your ground control points in the GCP manager. You can change the coordinate system of your ground control points in the GCP management window. To learn more about the GCP management widow, please read HERE Remember, your GCP coordinate system is the coordinate system in which these points were acquired in, this can be different and separate from your image and output coordinate system.
If you change the output coordinate system after completing a step, you do not need to reprocess step 1. You should re-optimize after selecting a new output system and this will remove the results from steps 2 and 3. You can then just process those steps depending on the needs of your project.
Alternatively, you could take the outputs from Pix4D and import them into some GIS software like ArcMap or QGIS and reproject to your desired coordinate system. You can read more about that procedure for QGIS at the link HERE.
After reviewing this info feel free to ask for clarification.