ECU remapping can be safe for engines if the re-mapped chip, or new chip, was programed by a reputable source. A remapped ECU will affect engine speed and load parameters, operating temperature, waste gate control, air intake, timing and fuel efficiency. All vehicles come from the factory with ECU maps that are “middle of the road” and yield the best emissions values, because they must meet federal guidelines. Your individual driving needs may be different, and remapping the ECU may be the way to go. Just ensure that the new program is suitable for your vehicle and engine type.
For more info, see Cheap Horsepower: Engine Performance Tuning