A Mechanic with an Inspection Authorization reports he performed an Annual Inspection on a Beech Bonanza A36 aircraft with an IO550 engine in June 2008. The owner recently informed him the engine should have been grounded at that time; because an Airworthiness Directive (AD); 2007-04-19R1; requiring removal of all the cylinders; was missed.

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Reporter stated that FAA Representatives in two different office locations; informed him they also; could not find the Beech Bonanza A36; engine Airworthiness Directive (AD); AD 2007-04-19R1 he was referring to; in their own FAA AD website. Reporter stated; because the engine AD was not under the engine section for AD's applicable to aircraft engines; the same AD would not even show up in the general section of applicable AD's. Instead that specific Beech Bonanza A36 aircraft with the IO550; were under the appliance section of AD's; and was the only one listed for Beech aircraft engines. Reporter stated the IO550 is an FAA approved STC; for that type of re-manufactured Continental engines. The engine provider of the IO550 has stated to him they use all Continental parts for the assembly. The software publisher sent him a letter; explaining they had to put that AD in the appliance section of their software; because the FAA listed that specific AD for the Beech A36; IO550 engine; in their appliance Section; not engine AD section.Reporter stated the FAA Representatives he had discussions with; can't explain why the FAA did not list that AD under the engine section and said they could not change where it was listed. But; they did asked him to go to FAA Headquarters in Washington;DC and explain the issue.