When I check the data source of map services authored by ArcGISPro documents, I usually get a reference to an msd file, which is not what I would like to see.
MXD-Authored map services ALWAYS return the on prem path of the mxd (not sd).
Sometimes, with ArcGISPro-Authored services, I get the on prem path to the aprx, but I don't know why.
Is there something I can do when publishing to ensure that the map service (service manifest) holds the map document path as the authoring document, rather than the msd?
What version of the software are you using? Starting with Server 10.1 .msd has been replaced with .ssdraft and .sd
Are you publishing to an RDS?
I just looked at a couple of my services and they are all reading the source as .aprx