By incorporating higher-form symmetries, we propose a refined definition of the theories obtained by compactification of the 6d $(2,0)$ theory on a three-manifold $M_3$. This generalization is applicable to both the 3d $mathcal{N}=2$ and $mathcal{N}=1$ supersymmetric reductions. An observable that is sensitive to the higher-form symmetries is the Witten index, which can be computed by counting solutions to a set of Bethe equations that are determined by $M_3$. This is carried out in detail for $M_3$ a Seifert manifold, where we compute a refined version of the Witten index. In the context of the 3d-3d correspondence, we complement this analysis in the dual topological theory, and determine the refined counting of flat connections on $M_3$, which matches the Witten index computation that takes the higher-form symmetries into account.
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