To be fair this seems to be more of a classic example of a documentation or training problem. Right from your link:
> During the mishap sequence, the MP started engines, perfomled an IBIT, and had a fully
functioning Flight Control System. Subsequently, the MP shut down engines to allow
maintenance personnel to service the Stored Energy System. During engine shut down,
the MA's Auxiliary Power System (APU) was running. The MP believed the APU
provided continuous power to the Flight Control System, and therefore another IBIT after
engine restart was unnecessary. This belief was based on academic training, technical
data system description, and was shared by most F/A-22 personnel interviewed during
the investigation.