Aha, thanks John. I just saw your message after sending my previous reply.
That would explain a couple of things - first, that the TCXO needs a workout, and may have been the entire cause all along, and second, that those Flash parts (or is it something else?) are used for storing data during operation. This greatly simplifies my view on how the pieces work together.
It just occurred to me that maybe the RTC chip (68HC68) has NVRAM inside, but no - I looked it up and see that its RAM needs battery backing too.
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