I've been trying to see if I can compile a list of all individual flown spacecraft, both flight-rated and test articles. (In doing so, I've noticed some discrepancies among sources... working on those.) No real reason to do so, other than my own curiosity.
I have observed that Apollo boilerplates were individually numbered/identified-- for instance, the Apollo A-002 mission launched on 8 Dec 1964, the Max Q abort test, used boilerplate capsule 23 (BP-23).
I haven't (yet) found that Mercury boilerplates were tracked in the same fashion. One source seems to indicate that the same boilerplate was used for all the Little Joe launches (?) but that obviously wouldn't account for the one on Big Joe, or the one from MR-BD (24 Mar 1961). Has anyone bumped into anything that identifies them individually?
(Interestingly, it appears that, although boilerplate Geminis did exist, none of them actually ever flew.)*
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* I'm only counting situations where a vehicle was lofted (or intended to be lofted) by a rocket as "flights." There may have been some drop tests of boilerplate Geminis, but I'm not interested in those.