By default, empty animation layers set to Additive mode get deleted when the scene file is saved and reloaded. You can override the default behavior in the MotionBuilder .History.txt file so that these layer are preserved when you save and reload the file.
This file in located in the MotionBuilder config folder of your user directory. For example:
C:\Users\<username>\Documents\MB\2017-x64\config.
RemoveEmptyLayer = Yes ;Remove empty animation layers that are in additive mode, without child or parent. (Yes/No).
Make the change to the line under the following headings: