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A (on-shell) quark has fixed mass. It's energy depens on the frame of reference you use for asking the question. Mass is a Lorentz scalar (i.e. is invariant). Energy is one component of the energy-momentum four-vector and is not invariant.

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The upper mass limit for a quark star depends on your assumptions and ranges between 1 and 2 solar masses (cf. this paper (arXiv link) from 2001). It seems to me that the reason for the similarity to neutron stars' mass range is that it both compact objects satisfy the TOV equation,  \frac{dp}{dr}=-\frac{G}{r^2}\left[\rho+\frac{p}{c^2}\right]\left[M+4\pi ...

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About the supposed paradox: $u$ and $\bar d$ have the same isospin quantum numbers, but not all the other properties. If you restrict your problem to only study the isospin space, you will not see that they have different charge and other different quantum numbers. About the charge: I don't know where your equation comes from, but it seems close to the ...

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