Hi Bekk,
I totally get that you're dealing with a bit of a mess with the double income statements due to the branch code change. Typically, you'd need to finalise the old code and clear out the pay history before moving to the new one. Since you're using an MYOB Business file, there isn't a way to fix this directly in the app. In this case, I'd suggest manually submitting the correct info and making adjustments directly with the ATO. I know it's not perfect, but it's the best move given the situation.
Feel free to get in touch if you need more help.
Cheers,
Princess