Hi Simon
I think the implementation you did on the site is confusing and wrong.
you consolidated ur au to the .com domain without specifying which folder or subdomainis the au section is.
previously because you have the .com.au in the domain Google understood that signal that this website is relevant to au visitors. but when you consolidated to the .com you need now to TELL or HINT to Google (through Google Webmaster Tools) where the whole domain that was targeting this country went.
and HREFLANG is not about Geotargeting but about the Language.