Hi there, @adamwyson,
I checked to see if there are any reported cases similar to yours, but I found none. Let's manually update your bank account three times to see if all transactions are uploaded to QBO. Here's how:
To temporarily complete your work, you can manually bring in transactions to correct the bank balance. Perform the steps below:
You will see the imported transactions under the For Review tab. I've added this article with the complete steps on how to use WebConnect: Manually upload transactions into QuickBooks Online.
Please let me know how it goes by leaving a comment below. I’ll be happy to help whenever you need one.