We study the rational Chow motives of certain moduli spaces of vector bundles on a smooth projective curve with additional structure (such as a parabolic structure or Higgs field). In the parabolic case, these moduli spaces depend on a choice of stability condition given by weights; our approach is to use explicit descriptions of variation of this stability condition in terms of simple birational transformations (standard flips/flops and Mukai flops) for which we understand the variation of the Chow motives. For moduli spaces of parabolic vector bundles, we describe the change in motive under wall-crossings, and for moduli spaces of parabolic Higgs bundles, we show the motive does not change under wall-crossings. Furthermore, we prove a motivic analogue of a classical theorem of Harder and Narasimhan relating the rational cohomology of moduli spaces of vector bundles with and without fixed determinant. For rank 2 vector bundles of odd degree, we obtain formulas for the rational Chow motives of moduli spaces of semistable vector bundles, moduli spaces of Higgs bundles and moduli spaces of parabolic (Higgs) bundles that are semistable with respect to a generic weight (all with and without fixed determinant).
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