If I recall correctly, the VATS is only designed to PREVENT the engine from starting if the incorrect key is used. If it malfunctions AFTER the engine is started, it should not shut the engine off due to safety reasons.
Not sure which years, but upto 95 I think, the VATS will prevent cranking of the engine. After 95, the VATS will ALLOW cranking, but not sure if it disables the injectors, or the fuel pump.
In the beginning of your post, you stated, "looses power". Are you referring to engine performance, or electrical power?