There is one piece that nobody appears to have picked up on:

Iona glanced at Corwin, received a nod, and replied, "Long-range submarine I-401."
"Four-oh-one! Huh. I thought you were scrapped," Tenryū said.

There-in lies an interesting possibility. Supposed the original shell of I-401 -was- scrapped, but the core was not? Placed back in stasis, left in a particular location, or whatever. That could explain why Miss James only had the single Core, and why it required a bit of work to reactivate. Also, if she was scrapped, Iona would then likely have been the -least- well-informed member of the group in terms of what happened after the war.

-Droken