I've been having similar problems. What I've learned is that removing the service from (a federated) server does not remove it from portal. You must remove it from both locations. Not the easiest workflow but oh well.
The exact error I get in Portal is:
Unable to reach the server where the service is. Consider using calling deleteItem with options = { 'force' : true } if the server won't be available anymore.
I found i was able to delete the items using the REST API as found in this thread here. So you're not really having to format the syntax, you're working with the Portal's rest interface.
For example, if you navigate to:
https://portalname/portal/sharing/rest/content/users/<username>/ you can see all the content and their IDs. you can then click on the ID title and then simply use the 'Delete Item' interface with the 'Force Deletion' option checked on.
This works in a more interactive way IMO although not being able to delete via Portal is clunky at best.
On a side note: this interface still isn't letting me delete orphaned items. I need to connect with my IT provider to get access to the location of the portal content directory to try to do this manually (this is an azure deployment so config and storage locations are not a simple file explorer procedure).
Let us know if that helps.