I have multiple geoprocessing services that copy an existing .aprx file to the scratch directory, do various things to the project (change data sources, zoom the map to certain locations, etc.), and then exports all of the layouts to PDF format. The service then returns a zip file with the maps and the .aprx file and associated geodatabase. Theses services are running on an ArcGIS Enterprise Portal 1.8.1. The PDF from the service look as intended. However, the .aprx file returned by the server is completely blank (no maps, layouts, etc.). When I run the same tool in ArcGIS Pro (before publish to a geoprocessing service) I get a working project and all maps and layouts every time. Why is the .aprx blank and what can I do to fix this?