The _General.AudioEngine_BasePitchHz setting exists in v4.2.0+ in the 'full' organ definition format for it:
If left at its default of zero, Hauptwerk will attempt to determine the base pitch automatically from the sample files, reading the mean pitch of all A-notes (for all ranks that the user hasn't disabled). Only set this to a non-zero value if you are certain that the value you specify is exactly correct, since an incorrect value would lead to the organ sounding at the wrong pitch (and probably being out of tune with other instruments and/or any real pipework).
There's no equivalent in the CODM organ definition format, I'm afraid. (The CODM compiles the above setting to 0.) However, as long as the pitches are stored correctly in the sample files, then the calculated base pitch should normally be correct.