Reconciled transactions now need to be manually matched but still showing as seperate transactions.

Hi there, @JB_Cog_SP.

There's no need for you to merge the transactions since the other one is already reconciled. You can delete the second transaction on your screenshot that was manually added to QuickBooks. Also, please take note that this process can only be applied if they are associated with the same accounts. 

Here's how to delete the transaction in the Bank register:

1. Go to the Transactions menu and click Banking.
2. Select the Bank account and click Go to bank register.
3. Click on the transaction and select Delete. This is how it looks like:

I've added this article in case you want to make changes on the reconciled transactions in the future: Undo or remove transactions from reconciliations in QuickBooks Online.

Please know that you can always tag my name in the comment section. I'd be happy to assist you further. Take care and have a wonderful day.