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if the battery is more than a few years old then I'd replace it as this sounds like the battery may have a faulty cell thats dropping the voltage below what the ECU needs to work correctly
low battery voltage will give all sorts of funny faults and this needs resolving 1st
Also check that the alternator is actually charging the battery in the car by taking a battery voltage reading with the engine off then another with the engine running. The 2nd reading should be higher than the 1st and climbing steadily. And also check that the alternator is secure to the engine as this provides the ground for the charging circuit and make sure that the engine / gearbox earth strap is secure and the contacts are clean and bright.
if the alternator appears not to be working - take it to a electrical specialist and ask them to test it as sometimes you can replace just the diode pack and this will repair the alternator without requiring replacement
if the window was working fine before the battery was discharged then I doubt that its suddenly gone bad as when the motors do go , its more of a gradual decline
yes I'd replace the battery as the next step and don't forget to check if its being charged when the engine runs
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