BAS Amendments should work IF the original BAS is in LodgeiT AND there are no values at PAYGI.
Once you've selected Amend, then be sure to use the Prefill option on the top Right of the form.
The status should now look like this
Now you can mark the form as lodged
Once you've marked the form as lodged, you'll see that at the bottom of the form, you have an amend option.
To get a BAS into LodgeiT not originally prepared in LodgeiT use the GST Analyser to 'call' the missing BAS.
Q: "Amend" button suddenly disappeared.
A: Possibly, you are in the incorrect form (Original) Check the dropdown arrow, it should the content of forms, ie "Original" and "Amendment". Choose the "Amendment".
In cases when the user creates an amendment and receive such an error on prelodge/lodge, the user must contact ATO directly. It seems ATO blocking amendment of the BAS for some reason.