KFC Exporter is a plugin for Blender that adds a tweaked fbx exporter to preserve the naming structure for compatibility with the persistence material data.
Use in conjunction with your
Blender has it's own indexing system that adds .001, 002 etc. to various objects and empties to give them unique names. This custom exporter removes .001 to .099 from the names of your object and texture before exporting into .fbx files.
To avoid a confusing issue with multiple same named materials it is advised that you rename those duplicated materials if you wish to preserve multiple copies.
You could also open a new document, or do Files > Clean up > Purge all (a few times) to remove unused material duplicates to avoid it all together.
You can check the details or help with the project on Github