Hi Cassie_T,
Thanks for laying that all out. It definitely makes sense, and you've already done a lot of the right things. From what you've described, the negative amount sitting in Prepare Electronic Payments is usually left behind when a bounced pay is reversed but the original payment batch wasn't cleared out completely. The fix is normally to go back into Prepare Electronic Payments and delete that negative transaction so things balance out again. Once that's gone, the reprocessed pay should sit nicely on its own.
For the super, you're spot on too. When a pay is reversed, the super does reverse as well, which is why you're seeing both a positive and negative amount for the same value. Unfortunately then can't be offset together, so the usual approach is to leave the negative one as is and only process/pay the correct (positive) super amount when you're ready. If anything still looks a bit off after that especially around the electronic payments, it might be worth jumping onto live chat support through our virtual assistant, MOCA, or submit a case via My Account so the team can take a closer look at the file with you and make sure everything's squeaky clean.
Regards,
Sai