This Article is about the BT521 Low Pass Filter feature.

Is it normal for the BT521 to read high or low impedance at opposite ends of a string of batteries when a rectifier is connected?

Yes, the rectifier can affect the BT521 ability to read the battery parameters. 

The Impedance results return to normal/expected across all the batteries when the rectifier is disconnected. 

Can the BT521 Low Pass Filter be damaged by the harmonic distortion from the rectifiers, causing harmonics to distort the voltage readings?

The rectifier will not damage the BT521. 

In review if the UPS is supporting power to a rectifier you need to use the BT521 Low Pass Filter.