I assume that you mean dead "pitches" that are the same on both manuals. The T-12 has a single set of oscillators producing a pure flute tone. A unit scheme lets you sound those flute notes at all manner of pitches, combined into synthetic diapasons, strings, and reeds. The oscillators are "keyed," which means they are not powered or running unless a key is depressed which requires a given oscillator to sound.
So, a dead pitch is simply an oscillator that does not"start up"when it is keyed. The culprit 90% of the time is the "keying capacitor" for that pitch. The giveaway is that the oscillator gives a tiny little "gulp" when keyed but never produces the steady tone. That symptom always indicates a bad keying cap.
You should contact Allen Organ and get the schematic. They will gladly sell you one for that analog organ. (Though they won't sell digital organ schematics to anyone besides their authorized techs.) The keying capacitors are located in a neat row, often covered over with a strip of masking tape, inside the metal generator chassis. You remove some screws, flip open the "lid" that holds the tuning coils, and see the keying caps lined up on an inside edge of the metal chassis.
(Be aware that there are two distinct styles of generator chassis. Most T-12 organs will have the old-fashioned metal pan with most components hidden inside. But the last ones built, from the late 60's into the 70's, have the "in-line" style, with the components laid out in a "staight-line" fashion on top of a phenolic board.)
Find thekeying capthat corresponds to the dead note. It will be 2, 5, 10, or 15 mfd. Replace, and the note should sound. You can even check it by clip-leading a new cap in without removing the old one, just to be sure that's going to fix it. Be sure to observe correct polarity. Electrolytic capscan EXPLODE if put in backwards.