All good Brent Jeal,
Happy to help.
I tried entering the opening balance for one of the employees in my test file following the article I shared previously, and you are right. The opening balances I entered shown up in the very next pay run I created after.
In this case, I would suggest you to contact Payroll support directly to get the best advice on how to handle the opening balances with your migration situation.
All you need to do is to find the blue "Payroll Support" button within the Employees session of your QBO file, and click on contact us. Our Payroll support team will get back to you via email soon after they got your message.
Please let us know how you go or if you require any additional assistance. Thank you.