The File and Document link report shows documents are attached on the map but when user check they are not found to be attached anywhere in the diagram.

The report generated at Nimbus should not be incorrect. There might be below possibility where the document can be attached to the Process map.

--> Generate the report File and Document Links which will display attachments to the Activities, Free texts, etc.
-->If the object is an activity the activity id will be fetched in the Activity ID column and if its Free text then text "Free Text" will be displayed in that column.
--> If it's a free text then there may be a possibility that it is hidden and kept on any symbol to fulfill attachment purpose. For Example, Knowledge Documents.
--> Select all the objects by pressing CTRL+A to find hidden free text.
--> Once it is pointed out you can check if any document is attached to it.
--> If not, try dragging the free text somewhere in the diagram area and check if any other free text is hidden behind the first one.

Using the above method you can find the document attached to the hidden free text. If the user is still not able to find attached document then the user may raise a support case for further investigation.

Note: If there two free texts one on the other then you can use the "Send to Back" and "Bring to Front" buttons on the menu ribbon to send back the other free text to the back and bring the free text to the front where document is attached respectively.