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Do you know of any real life cases, when invalid FMS data affected somehow the flight operations?

By invalid FMS data I mean a case, when the procedure coding does not reflect properly the original procedure as published by state's AIP service.

Related question: What happens with RNAV procedures on the way from AIP publication to FMS database

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Here is some old material used in Europe to prepare for the transition from AIS to AIM: AIS to AIM: Enabling the Net-Centric Information Environment by Roderick van Dam, Head of Eurocontrol Legal Service. The document references two legal cases where navigational data and hardware were involved.

Pakistan International Airlines

Bejon v. Pakistan International Airlines (Toulouse Court of Appeal, 1998) Liability of Jeppesen raised. Jeppesen argued that approach map was based on map provided by States. Court concluded that map was technically acceptable This case confirmed the risk related to the publication of Aeronautical data.

More: PIA Flight 268.

American Airlines

American Airlines v. Jeppesen- Anderson and Honeywell (US Federal Court, 2000) The Accident Report had concluded: the probable causes of the accident were related to failures of the flight crew; contributing factor was related to FMS-generated navigational information; AA blamed the Jeppesen software in the Honeywell computer; alleged that products helped caused the crash; A Federal Jury found that Jeppesen was 17% at fault and Honeywell 8 % at fault.

More: American Airlines Flight 965.

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