Hi there, @bluebonnetapts.
Thank you for reaching out to us. I can share some information about why the payment transactions are duplicating in QuickBooks Online.
Currently, there's an open investigation regarding payments duplicating (INV-19995). Our engineers are working for an immediate fix.
While waiting for the resolution, we'll need to add you to the list of affected users. I suggest contacting our QuickBooks Online Support Team so we can get your company set up for email updates.
Thanks for your understanding and patience.
I'll also get back to you personally once I get an update. Feel free to visit the Community site if you have questions about QuickBooks.