You definitely do not want to un-federate your site. For us, pro puts everything in it's 'SharedProcesses' folder that is part of your desktop user profile, like:
C:\Users\username\AppData\Local\ESRI\ArcGISPro\Staging\SharingProcesses\0001
and in that directory you will see sdddraft, sharingInfo.json, etc etc. All of that gets written to the
...\\directories\arcgissystem\arcgisinput\YourServerFolder\YourMapName.MapServer\extracted\p20
directory, for example
For me, I made sure I shared my profile path above with the arcgisserver domain account so that Pro would not have any issues writing from the SharingProcesses folder to the ...\arcgisinput\... folders. Since I did that I haven't had any issues overwriting traditional map services to my federated site.
I don't know if named user vs concurent use licensing affects any of this. We use concurrent.