5.3v charger

[drgeoff]

I could simply turn off the warning but I'm afraid I'm slowly killing my Pi in the meantime.

Low voltage is not detrimental to your RPi, so do not be overly worried about that.

It is theoretically possible that low voltage could result in corruption of the file system on the SD card or USB drives but I wouldn't expect that to be permanent hardware damage.

[Burngate]

Disconnecting the harddrive DOES make difference, but it's weird: the rainbow icon stays visible all the time. However, when I reconnect the harddrive the same old behaviour appears: it fades away and every now and then it lights up shortly.

It's possible the power supply for the drive is back-feeding the Pi.