An option for "Interrupt Mitigation". This would work so that if it's checked, similar to auto-turns, the game wouldn't stop until the desired increment happened. This would work by saving the desired increment length and adding up the time that had passed each subpulse and if an NPR interrupt happened, the game would immediately click an increment button and continue to do so until the desired time had passed. The idea is to circumvent the fact that NPRs need new increments to think.
Example: Player clicks 5 days. An NPR gets detected by another NPR at 2 days 6 hours. Since "Interrupt Mitigation" is checked, the game will click 1 day. The NPR ship gets undetected at 2 days 12 hours. Step 3) repeats twice. Now that the time is at 4 days 12 hours, and that's less than 24 hours, the game clicks (whatever is most efficient, probably 8 hours). And so becoming smaller and smaller until the elapsed time is 5 days, where the game stops.
This might require tagging events to see which ones interrupt this sequence, or just use whatever controls if the event is visible.
Feedback appreciated! Will read tomorrow.