A question came up today at my office asking whether ArcGIS Server map or feature services read or somehow access the ArcGIS Pro project file that was used to publish them on an ongoing basis. My understanding is that once they are published, they don't read or access the Pro project file, but I wasn't 100% sure. I am hoping someone can clarify this. Currently, my system is a standalone ArcGIS Server on version 10.9.1. Thank you.
When you publish a copy of your map is copied into the server directory. It is not the aprx, just the map you published from it.
After you published you can delete the aprx you used but it is a good idea to keep it so if you need small changes you can use it to overwrite the service.
Have fun