Document reference "File not found" and attachment symbol(paperclip) are still visible on the diagram after document deletion with the option "Delete document link and file" which removes the document completely. To resolve this you can follow the below resolution.  

Steps to remove deleted document reference from the process map,
1) When a single document added on a single known activity.
--> Open Author client 
--> Open process diagram
--> Right click on the attachment symbol on the activity where the deleted document was present
--> Click on Access/ Modify
--> Select the deleted document.
--> Click on the delete document.

2) When the document is added to the multiple activities on the process map.
--> Open Author client 
--> Open process diagram
--> Go to Map -> Map Properties
--> Click on the "Remove Broken File Links" button on the Options tab.
--> Click on yes button
--> This should remove all the invalid references from the process map.

Note: If the document is present on the multiple process maps then you have to follow the 2nd step for each process map.