Protective diode across dump load
The 25PV045 Schottky diode will die as soon as you apply an input voltage greater than 45 volts and the relay/MOSFET switches on. This is because its maximum voltage rating is only 45 volts and according to your schematic you may have 600 volts at the input.


  My question is when the Schottky is in flyback mode will any of the
  current go through the small diode and perhaps damage it or will
  resistor R68 prevent this?


Given that the main diode is likely dead, any inductive kick-back current will force its way through the 1N4148 and the 200 k resistor and probably damage the resistor. Now your LED circuit is fairly functionally dead.