I think there is a problem with this experiment.
When your photons enter the "down converters" they are interacting, in effect being measured and are no longer necesarilly in the same quantum state. The same thing happens when you manipulate the photons to merge them or not.
However let's assume we could fix these problems and put that on one side this seems a variation of the EPR paradox.
I'm guessing you've come across this but for those who've not you have the emission of two photons in the same quantum state, when one is measured the other appears to change state simultaneously despite apparent light years of separation.
http://en.wikipedia.org/wiki/EPR_paradox
Because this appears to be faster than light travel it can be seen as time travel (the two concepts are deeply linked)
The Photons are in what is known as a quantum entangled state
http://en.wikipedia.org/wiki/Quantum_entanglem ent
Now we come to what you're not going to like.
When you talk of explaining and Quantum Mechanics you're suddenly on very shakey ground QM doesn't explain what is going on, it gives you very powerful tools to predict the outcome.
There are numerous attempts to describe the underlying "nature" of such things these are known as
Interpretations Such as the Copenhagen, the Many worlds and the Bohm
I'll let you investigate these because there's far too much for an AB reply