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It honestly just wasnt talked about, wasnt acknowledged at all, even to parts of the Navy, and especially the Army. Its even debatable how much the Emperor even understood about the scale of the losses.
Upon its return, Kido Butai's wounded were kept secluded in special wards and facilities, with communication heavily screened, and leave very hard to come by, the wounded were even transfered from warships that had returned at night to keep it underwraps. Those air crew, or now orphaned ships company who didnt have immediate new orders often went to a training command, but in the coming year many would see a return to service as the Solomons consumed more and more units of the IJN. And in all cases were ordered not to discuss what they knew, if anything of the true scale of the losses, and the orthodox story quickly propagated so everyone was aware of what line they had to toe.
It took over a day for Hirohito to even be told of a rough sketch of the losses suffered at Midway once the Naval General Staff got word from the Combined Fleet, and even then initially it was 2 CV's sunk and 2 badly damaged. With a more complete picture only being presented during a full day of meetings on June 8, when His Highness famously instructed the Navy to not allow the loss to compromise its offensive spirit.
On June 10 then a public statement was put out by the Navy Department, admitting the loss of only a single carrier, and another damaged, for the sinking of 2 US carriers. The second part is basically what the IJN believed as it wasnt clear that the one I-168 bagged was the same as the one or ones hit the day before. What was a bigger issue though is that at a Joint Army-Navy conference to go over ongoing matters, the Navy never told the Army the full extent of their losses, another example of the horrible state of service relations at the time. This decision to report those losses were started as high as Admiral Ugaki who was Yamamoto's Chief of Staff, and would be codified by later memo's Those killed would also only gradually receive notification over the coming months, and without reference to the ship he was on.
Kaga and Soryu would then officially be removed from the Navy List on 10 August, acknowledging their loss or being so damaged as to be useless. Akagi, and Hiryu were kept on the list but without any crew assigned and finally removed in late September.
Islands of Destiny by Prados
Shattered Sword by Parshall and Tully