Numen tries both, a ref id first, then falls back to a base id. 096BCE.txt is the correct file name for Boone. You should see in Numen.log in the game directory that it's been loaded. The prompt might be something like "You don't doubt and obey your superior", but since you already have a prior history this may result in a mess. You may want to cleanup his context in {GameDir}\Numen\NPCContext\FalloutNV.esm\096BCE.txt
096BCE.txt is the correct file name for Boone. You should see in Numen.log in the game directory that it's been loaded.
The prompt might be something like "You don't doubt and obey your superior", but since you already have a prior history this may result in a mess. You may want to cleanup his context in {GameDir}\Numen\NPCContext\FalloutNV.esm\096BCE.txt