A dual fuel common rail system may be operated in a regular mode in which a relatively large charge of gaseous fuel is ignited by compression igniting a relatively small injection quantity of liquid diesel fuel. The dual fuel system may be operated in a single fuel limp home mode in which liquid diesel fuel is injected at higher pressures. When transitioning from the single fuel limp home mode to the dual fuel regular mode, accumulated leaked liquid fuel in the gaseous nozzle chamber of each fuel injector is purged and burned in the respective engine cylinder.