Here is our configuration: HA Portal Windows 2016 and at 10.6.
We have turned off the ability of users to publish Map Image Layers after noticing that the ArcSOC's were consuming all the RAM and causing performance issues with our Portal. Our understanding in discussions with support that this is expected behavior when users publish from ArcGIS Pro, that they services end up published on the /root/ of yoru server. Anyhow since that change users have 'deleted' those offedning layers from Portal, but ArcGIS Server still lists them as being available on the root of the server (Manager/Admin API), but I noticed in looking at the json today that there is a section which reports on if they are connected or disconnected from Portal. I would like to know if I can delete these services as the users can't see them through Portal anymore, but they still exist in Server. Inside the Admin API I can see where I can delete them, but I didn't want to just start deleting services without checking first. These MIL still have ArcSOC's running on the servers inside Task Manager.
If you publish a non-hosted service to a federated Server, it creates an item in the portal as you know. If you delete the item in Portal, it won't delete the service. However, if you delete the service, it will delete the item in Portal.
On the other hand, if you publish a hosted service, deleting the service won't delete the item, but deleting the item will delete the hosted service.
If you're sure those services are pointing to the items that were deleted, the services can be deleted.
This behavior has changed as of 10.6.1:
The deleteItem operation has changed at 10.6.1 so that when a service item that references a published service on a federated server is deleted, the corresponding service is also deleted from the server. If the item represents a capability for a service, like WMS, then the capability will be removed from its parent map service.