I called my super fund about why my voluntary contribution wasn’t showing up in my ATO profile and had been changed to $0 in my in-progress tax return - they advised me that it was strange and they definitely notified the ATO about my contribution and to just wait and see if it resolves in the next few days as things could change while the processing is in progress.

They also reassured me that if the ATO finalise the tax return without my contribution, I can get it amended and provide the documentation I received from my super fund, so I WILL get a refund instead of a bill eventually, but that will be annoying because I don’t know how long it will take to process. I’m relieved I have this bonus money coming through because at least I can move on with my life