In recoil proton scintillators, the hydrogen acts as a neutron converter to produce protons when a neutron strikes a H atom. But what happens to the electron in H atom? Where does it go? Does it remain a free electron?
Scintillators aren't generally made of pure hydrogen; the hydrogen is either covalently bonded to some large molecule or otherwise bound up in the crystal structure of the solid.
If incoming radiation, such as a neutron, knocks a proton free, the proton generally leaves its associated electron behind. So organic scintillators that react this way would have a large neutral molecule turn into a slightly-less-large molecule with net negative charge, due to the missing proton. A crystalline scintillator which underwent proton recoil (though I'm not sure there is such a thing) would, for some amount of time, have an extra electron at the site of the recoil. The relaxation of both of these processed back to equilibrium is generally what produces the scintillation light which actually reaches your detector.
Given that the ionisation energy in a solid is of the order of a few eV and that the energy of the incoming neutron (and recoil proton) is of the order of several MeV, there is a lot more than the initial electron to worry about. The recoil proton causes a shower of ionised particles in the detector. It is the re-combination of these millions of electron-ion pairs that produces the photons that we "see" with the photo-multiplier tube.
So I don't think you can say for any certainty what happens to the original electron. It just jumps around in the lattice until it finally finds an orbital to call home.