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We've been saying this for three weeks. The OP hasn't budged.PeterDonis said:Once more, "single photons" is not a good way to think about what is going on in the case of very low intensity.
Where I think he's going is that if a photon goes into the apparatus, and a photon of the same energy comes out of the apparatus, any explanation involving energy transferred to the medium cannot be right because there is no energy to do it. (If this is not the OP's position, I urge him to write more clearly and specifically)
Unfortunately, the OPs description is a hodgepodge of classical and quantum. It suffers from not proposing a specific configuration and a specific set of measurements (for example, one does not measure velocity so much a sposition and time.)
Without clarification, I can only speculate, but I am unconvinced that even with a single photon state in you get a single photon state out. Even in those case where you do, the medium can still transfer energy to and from the electromagnetic field without violating anything. What it might be doing whenn it is not being measured is not something addressibnle by QM, or arguably by science.
But let's hope we don't go three more weeks.