10.09.00.74 (Update-9)
Nested reference files cannot modify via Level Manager in active file. Levels of nested reference file are greyed out. This wiki article will help to activate the editing option and change the color of nested reference file without performing changes to the master file.
If above problem still persists, then please create a Service Request and contact the Bentley Product Advantage group. Please include a list of all relevant details to get in depth analysis for a solution or workaround