I like to see a diagram to understand what you are doing AND how the diode can blow. Here are my thoughts.
1) Reconsider having a dual large battery starter idea, it may not be necessary, adding weight and complexity, with undesirable failure mode. The #2 battery can be much smaller, with the intent to provide a second independant power source for essential in-flight electrical systems.
2) At no time should you be worried about blowing a diode.
1) Two full size batteries to have extra crank power will add weight and complexity. A good battery, starter and engine in good repair, makes starting on one battery routine, minimizing the value of dual batteries. Typically the #2 battery for the E-bus (essential bus) is a small battery, eg 7.5 Ahr (for weight and size) and good to drive the emergency or essential bus for +45 minutes. The whole idea is to isolate EFIS and or Elect Ignition for min flight power until you can get on the ground.
You might consider battery terminals accessible from cockpit or outside fuselage so you can attach a battery charger, without removing a lot of access panels. If you end up with dead battery you can charge it. Another tried and true design (to add battery to start) is an external AUX jack or receptacle (AN2551, MS3506-1) to charge or jump the airplane with dead battery. You can carry one of those Li-ion jump packs. I'm not a fan of jumping a totally dead battery, puts a heavy strain on the alternator. When jumping of make sure polarity is correct, check and double check. Don't trust FBO ramp'er.
https://www.aircraftspruce.com/cate...p/menus/el/jumpercablesplugs_receptacles.html
2) A Schottky diode as you know is a one way valve. In the Fwd mode you get 0.5 volt drop. In the reverse mode you get 100% voltage drop... Schottky come in ratings to handle +100 of amps. Typically (in my mind) the Schottky diode allows the main bus (alternator) to charge the second battery (E-bus), but it keeps the second battery from being drained by main bus (one way flow). The Schottky diode connecting the #2 battery main bus will see little or no current when starting. As you said you will provide second battery contractor (relay) to parallel #2 battery for starting (IMHO not needed). Relay, switch, heavy gauge wires to do this adds weight, complexity and cost. One way you might overload diode fwd current rating is due to battery charging + bus load. I doubt a battery charging will ever take more than 15 amps. You should not have more than 15 amps load on the E-bus (EFIS, EIS, EI, Com). 30 Amp should be enough, but you should run engine until current drops down before turning off your parallel relay.
Another way to go is use the EFIS and Electronic ignition (CPI2) back up batteries integral to their design... A lot of electrical items now have their own back up scheme...