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Yes it ran after it was reprogrammed but not in Toyota. The technician was formerly from Toyota and claimed he brought the ECU to Autoworks along EDSA. What are the risks of having an ECU that was reprogrammed? Toyota said they're no longer manufacture 1999 ECU and had to be outsourced.
There shouldn't be any risk at all as long as it was reprogrammed with the right equipment. I don't know if your ECU was reprogrammed before and I assume that it's still the original ECU that came with your vehicle because it's not often that we'd hear an original ECU's software going bad and needs to be reprogrammed. Usually, a component inside would burn out or the ECU will get damage from flood. At least, your problem got solved.