At the start of Mass Effect 3 it is revealed that roughly six months have passed since the end of Mass Effect 2. During this time the Normandy SR2 has been in dry dock being refitted.
During this refit period one would assume that the Alliance would want to remove any possible Cerberus security breaches. Any incumbent computer systems, VI/AIs included, would seem to be prime suspects for any hidden Cerberus traps or back doors. Thus one of the first things I would expect Alliance Techs to do, in cleaning out any bugs, would be a complete wipe of the computer systems and installation of the latest Alliance programs and VIs.
What was the Alliance's reasoning behind not wiping the Normandy's computer systems (and consequently not deleting EDI)?