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I have a 2007 Lexus GS450H that has a new hybrid Battery pack I installed back in August. It even has a new engine because the older one had gone bad. A few weeks ago, the car gave out a check hybrid system warning on the cluster and the arrows on the energy monitor disappeared and I could hear the hybrid cooling fan operating at maximum speed. 5 mins later, the VSC check light came on aswell. I scanned the codes and I found there were 2 fault codes: PA084 - Battery cooling fan 1 circuit low and P3177 - Transmission Oil pump motor coil temperature sensor circuit high. 

I therefore, reconnected the connection to the oil pump motor located on the gearbox and the p3177 code disappeared. I put in a new cooling fan too but the pa084 code didn't go away. A few days later, the P3177 code came back. I've now got both the codes on my car. I've tried disconnecting the 12v Battery for 5 mins and reconnecting but even that has not helped. What could be the issue?

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For the circuit to go high, the sensor has been disconnected, the sensor has failed open circuit, the wiring is damaged/shorted or there is a problem with the ECU.

It is worth measuring the resistance of the sensor across the two terminals at the pump to make sure you don't have 0 or infinity ohms.

Given that you had two, somewhat unrelated, errors I'd check the connections on the main ECU - maybe reseat those/check for corrosion on the pins.

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Do you think it's fine if I just flashed the codes permanently and got rid of the check hybrid system error instead of going through the procedure of checking the wiring. Because the hybrid system is totally fine. It's delivering the right amount of power and there is no abnormal discharging or charging. These codes are NOT affecting the drive in anyway whatsoever 

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Certainly clear all the code, if they don't come back then it was possibly just a spurious event. Was your 12v Battery a bit flat at the time perhaps?

If there is a problem then the faults will come back at which point you will need to investigate further.

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UPDATE:

The error went away for 20 minutes. I did a couple of small hard acceleration runs and it was all fine. Just when I pulled up to my driveway, it popped up again. I'm going to a mechanic tomorrow to get it permanently go away with the help of a flasher

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If you've cleared it with a reader, then it was cleared.

It means the system is detecting a new error. Not something that is likely to be resolved that easily I'm afraid.
So long as the error code is stored, the warning light displays, so if that went off, the code had been flashed already.

The car does do self-diagnostics which resets code so you may have an intermittent issue.

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