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We derive universal constraints on $(1+1)d$ rational conformal field theories (CFTs) that can arise as transitions between topological theories protected by a global symmetry. The deformation away from criticality to the trivially gapped phase is driven by a symmetry preserving relevant deformation and under renormalization group flow defines a conformal boundary condition of the CFT. When a CFT can make a transition between distinct trivially gapped phases the spectrum of the CFT quantized on an interval with the associated boundary conditions has degeneracies at each energy level. Using techniques from boundary CFT and modular invariance, we derive universal inequalities on all such degeneracies, including those of the ground state. This establishes a symmetry enriched $c$-theorem, effectively a lower bound on the central charge which is strictly positive, for this class of CFTs and symmetry protected flows. We illustrate our results for the case of flows protected by $SU(M)/\mathbb{Z}_{M}$ symmetry. In this case, all SPT transitions can arise from the WZW model $SU(M)_{1},$ and we develop a dictionary between conformal boundary conditions and relevant operators.