I went through a similar scenario with the D4 a few years ago. The red flashing light was simply the EVC saying it is now locked. I bought the boat without receiving the FOBs. Boat EVC locked itself due to low voltage on the engine battery and thus I suddenly had no ability to start engine. My boat had also not gotten needed software updates, and nothing would correctly load, to include programming a new FOB. Diagnostics showed a bad throttle quadrant, replaced - then the EVC would not work correctly, replaced that too. Hopefully your issue will be resolved with simple programming, not part replacement.
One important tidbit my mechanic articulated to me. If you don't lock your engine with the FOB, the EVC is simply going into a "sleep mode" - and turning off the battery while the engine electronics are just sleeping (vice being turned off by the FOB) is not healthy. So, it is not just about locking the engine so the boat can't be stolen - it also impacts how the electronics boot up and he highly recommended locking out the engine with the FOB before turning off the engine battery switch.
Good luck with your fix.