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We investigate the effect of blinking on the two-photon interference measurement from two independent quantum emitters. We find that blinking significantly alters the statistics in the second-order intensity correlation function g and the outcome of two-photon interference measurements performed with independent quantum emitters. We theoretically demonstrate that the presence of blinking can be experimentally recognized by a deviation from the g value when distinguishable photons impinge on a beam splitter. Our results show that blinking imposes a mandatory cross-check measurement to correctly estimate the degree of indistinguishablility of photons emitted by independent quantum emitters.

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