Ya not all tom and chill plants produce crops that finish at the same time. If you flushed some varieties the next developing fruits would be so deficient and stall.
Id just avoid flushing fruit and veg and leave the flush stuff to weed sites full stop, they have their own practices that arent so stupid and have been done for a very long time.
Id actually not let my toms soil go bone dry either, just crack and screw the toms
Seriously, they'll be safe to eat. Some people actually stress their hot peppers to make them hotter. That includes feeding them very little if anything at all, letting them go dry, abusing the plants, etc...