I guess I am not sure why it would be doing this for you.   I have logged over 400 flight hours doing tactical/assault type landings in a VSOA and never once had the engines shutdown after reverse.   Could be how the throttles are set up.

I use two saitek throttle quadrants with J2 as Engine1, J3 as Engine 2, J4 as Engine3 and J5 as engine4.  J1 is set up as spoilers (or as in the C-130 air deflector doors).   J6 is set up as Flaps lever.   I use a CH throttle quadrant as my condition levers and switches 2-5 (UP) as fuel cutoff.    

I set up FSUIPC to when in reverse detent it will use the "Buttons + Switches"  Put Engine 1 in reverse and under right side...
Throttle 1 Decr have the control to repeart while held checked and Throttle 1 Cut when sent when button relased and repeat for other 3.