Their manuals have indeed had some flaws - as have other airlines' manuals - which is what the new SAI process is intended to discover and correct. The problem with the other airlines certified under the previous system before SAIs (Safety Attributes Inspection) is that there was no systematic way of discovering and fixing any flaws in their manuals. Now there is with the SAI process, but it is an exponentially more burdensome process for both applicant and FAA with the SAIs than ever before.
Atlas Airlines, an already certified cargo carrier, was the first and only other airline to go through the SAI process when they decided to upgrade from cargo-only to passenger service. They went through a partial re-certification. For that EXISTING carrier, going through their re-certification for their upgrade to passenger service took two years.
Before SAIs, it took 6-9 months for an airline to get certified under the old system. So it's a whole new world under SAIs.
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