When you are updating your machine credential or keystore password, upon clicking Ok, you will be prompted to restart HandiTax.
Close out of HandiTax.
Log back in to HandiTax.
The credentials will now be applied.
Important: Do not go back into the set ATO credentials window. When you log back in to HandiTax, you should be able to lodge or prefill the tax return if the ATO credentials are valid.