I tried to open some of your orthophotos in QGIS (one which was correctly georeferenced and another one which was not). I first imported the one that had no issues and it looks like a user-defined Coordinate System is recognized. Then I opened a new session of QGIS and I opened an orthophoto that was giving issues and it looks like it does not have any coordinate system defined; QGIS suggests me the recently used coordinate system (the one defined by you) and I select that one.
I was able to restore the right coordinate system for the output opening it in QGIS. After importing the GeoTIFF file and selected the user-defined CS as explained above, right-click on the layer in the Layers panel, Export > Save as and select as ouput mode Rendered image , give it a name and select the destination folder. Once done, you can replace the orthomosaic with wrong geolocation with this last one directly in the Cloud interface. Having no coordinate system defined, the Cloud was defining an arbitrary coordinate system for the project when importing it.
What could have caused the issue:
Definition of a different and wrong output coordinate system
Editing of the orthomosaic file in other third-party software
Issue with calibration in the project processed on the desktop application. If this is the case, you can open a ticket and send me the p4d file and the quality report (pdf), so that I can investigate further.