I had a similar issue when first hired at my org to do some administrative work on their enterprise. A previous user had one orphaned item that didn't appear in Portal. ESRI Support gave the following steps:
- Navigate to Portal Sharing rest: https://portalURL/webadaptor/sharing/REST
- Replace portalURL with your org's URL and webadaptor with the name of your webadaptor
- Login as admin
- Click on Community > Users
- In the User Search box, type in the username. Click Search User
- Click on the user account
- Search for User Content option at the very bottom of the page. Click on it
From here I had to copy down the itemID for any orphaned items. At the bottom of the page listing those items there was an option to delete items. You click on that item and you can put in the copied itemID's (one at a time I think) and delete them. I can't say for sure but there may also have been an option to move those items (potentially to another user??) but if they are orphaned then I have no clue what that would even really do.
Anyway, this may not be useful to anyone but just in case it is, I figured I would post it.
Casey Carpenter
