Looks like what it does is erase every command under a master command. If you have two master commands, it doesn't erase them both, just the one. Here's how to make it erase the file:
1. Click "Create new settings file"
2. Click on a master command
3. Click on the "+" of that master command
4. Click on the child command you want to erase
5. Click "delete" command
It will erase ALL of the commands, including that master command.