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Are you sure that cap couldn't be a power filter cap?
That's most likely what it is, statistically speaking. I'm basing that on an assumption that decoupling (a.k.a. bypass) is the most common use of ceramic caps. I could be wrong, or your iPod could be an atypical user of ceramic caps.
A well-engnineered system is designed so that every last decoupling cap isn't absolutely required for the device to function at all. You want to overengineer things a bit, for lots of reasons, not just the unlikely possibility that one will be knocked off the board. Apple knows how to do proper engineering.
If instead your iPod started but crashed shortly after startup, that'd be different. I'm not saying the cap is pointless so removing it is totally harmless, just that there are reasons why removing it should not be expected to completely brick the iPod.
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completing the circuit with the hdd...
I doubt it. Coupling caps are an analog filtering type function. Failure to boot is a digital-domain problem, which is all about DC. There shouldn't be any coupling caps in that section of the circuit.
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Or be part of a voltage regulation circuit for the hdd?
A much better theory, though probably less statistically likely than mine.
I don't see any need to tie it directly to the HDD. It could be a filtering cap for the DC-DC converter that turns the 5 V USB power into something more like 3.3 V for the main processor, for example. Losing that could certainly kill the device.
Edited by tangent - 5/25/10 at 6:39pm