You can delete history on a model deformed with the Muscle deformer, but it is important to use the Safe Delete History option in order to avoid deleting Muscle or other connected nodes automatically.

To safely delete muscle history

1. Select the object you want to delete history for.
2. Select Muscle > Skin Setup > Safe Delete History from the main menu bar.

   The Muscle system first disconnects the nodes from the selected object, then deletes the history.