You may experience this error in the Revit addin:

You can use Deep Space dashboards to diagnose the problem.

For example, an identical BIM360 file name may be present, and appear like this:

If you have loaded BIM360 file data to Deep Space, you can observe these duplicates in our File Name Audit dashboards:

Solution 1:

In Revit, it may be advisable to Unload the duplicate link from your Federated Model and re-checking the Revit addin Configuration. Is the Duplicate link now gone?

Solution 2:

You may be able to rectify long term by deleting the duplicate file on BIM360:

Then proceed to Reconfigure the files using the Revit addin.