To get a BAS into LodgeiT not originally prepared in LodgeiT use the GST Analyser to 'call' the missing BAS.

Pull the activity statements from ATO portal (since the form has been already lodged). Please follow this guide on how to - Collecting Activity Statement (AS) - not showing in LodgeiT. 

BAS Amendments should work IF the original BAS is in LodgeiT AND there are no values at PAYGI.