This paper presents the second part of the research activities carried out to develop a novel Global Navigation Satellite System (GNSS) Avionics-Based Integrity Augmentation (ABIA) system for manned and Unmanned Aerial Vehicle (UAV) applications. The ABIA system's architecture was developed to allow real-time avoidance of safety-critical flight conditions and fast recovery of the required navigation performance in case of GNSS data losses. In more detail, our novel ABIA system addresses all four cornerstones of GNSS integrity augmentation in mission- and safety-critical avionics applications: prediction (caution flags), avoidance (optimal flight path guidance), reaction (warning flags) and correction (recovery flight path guidance). Part 1 (Sabatini et al., 2012) presented the ABIA concept, architecture and key mathematical models used to describe GNSS integrity issues in aircraft applications. This second part addresses the ABIA caution and warning integrity flags criteria and presents the results of a simulation case study performed on the TORNADO Interdiction and Strike (IDS) aircraft.