I create an entangled photon pair. One photon is sent inside a resonant cavity which reflects the photon many number of times. Will there be decoherence between photon in the resonant cavity and its entangled partner? If yes why should it happen? Also is decoherence affected by type of surface of mirror i.e Glass Vs Metal.
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No, since mirrors don't cancel the wavyness and preserve phase.
Same for simple transport in a medium (having a refraction index), BTW.

Fabrice NEYRET
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what about change of transport medium - change of refractive index multiple times? – user43794 Mar 08 '16 at 19:32
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same thing, as long as there is only elastic interactions. refraction is basically a wave behavior. – Fabrice NEYRET Mar 08 '16 at 20:54
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Will passing entangled photon through a nonlinear crystal destroy its wavyness? My point is change in energy of photon should destroy/lessen coherence. Mirrors do not affect photon energy therefore entanglement is safe. But what about cases where there is change in energy? Is there any book/article which discusses decoherence in entangled particles specifically? – user43794 Mar 09 '16 at 03:20
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what kind of non-linearity do you have in mind ? But yes, change of energy sounds like something inelastic. (But it gets beyond my knowledge). – Fabrice NEYRET Mar 09 '16 at 04:42
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Beside, don't forget all the interactions occurring with virtual particles in the quantum vacuum ! If they weren't elastic most of the time, practical entanglement would just be impossible. – Fabrice NEYRET Mar 09 '16 at 07:01