By default, Reactor checks whether all changing atoms of the reaction are mapped, and if not, then maps all atoms (original atom maps are preserved, only unmapped atoms will be mapped). When the command line parameter --skip-reaction-mapping-check (-A) is specified, mapping of the (input) reaction will not be checked.
If the command line parameter --map-result is specified, then the resulting reaction will be mapped. The possible mapping styles are listed below:
"changing": map all changing atoms (ChemAxon style), all changing atoms will be mapped
"matching": map all matching atoms (Daylight style, all atoms will be mapped, except orphan atoms)
"complete": map all atoms
Read more about reaction mapping.