For what it's worth, every time I recover a vessel (even ones that completely unscathed) it kills all the kerbals aboard. Or if it doesn't kill them, maybe they resign in protest, never to fly again. I don't know. It just seems that for whatever reason for me, kerbals only fly once in KSP2. (I'm sure it's just a bug that will be fixed soon).
If the kerbal in question hasn't been "recovered" (i.e., killed) yet, and you're building multiple vessels in the VAB, check all the vessels you're working on in the VAB. The kerbal might be hiding in a command pod.
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I don't know much about how they are stored in the JSON save files, but here's something I've noticed.
In terms of the save file specifics, I've noticed that if the kerbal in question is a main kerbal (e.g., "BILL_KERMAN", "BOB_KERMAN", "VALENTINA_KERMAN", "JEBEDIAH_KERMAN", or "TIM_C_KERMAN"), and alive, they'll be in both KerbalData {Kerbals {} } and KerbalData {CustomKerbals {} }.
But if they are recoverd (killed), they are removed from both of those and placed in KerbalData {CustomKerbalRefresh {} }
I'm guessing -- although I don't know for sure -- that if the kerbal in question is not one of the main kerbals, and is just a random kerbal, and is recovered (killed) , then that kerbal is simply removed from the save file altogether.
Have you tried searching the save file for the kerbal's name?
(Nevermind. I see you solved it.)