I appreciate you for sharing what works on your end to match your transactions in QuickBooks Online (QBO), @XL_Velo. With this, I'm here to share further details about this matter.

QuickBooks downloads transactions based on the data provided by your Square app. Based on your scenario above, I can see no downside in updating your older transactions with the appropriate account. I agree that by the time you've changed the settings to the new account, your past charges were updated as well. So changing the account back to the old one in the bank deposit section is the proper way to resolve the issue.

You're already on the right track in categorizing and matching your downloaded transactions in QBO. Doing so will keep your account updated and avoid duplicates. You just have to thoroughly check their details to match them to the appropriate ones.

Also, syncing Square with QBO makes it easy for you in managing your sales. To make sure your financial data is accurate, I'd recommend reconciling your Square account every month. This will effectively monitor your income and detect any possible errors accordingly. For the step-by-step guide, you can refer to this article: Reconcile an account in QuickBooks Online.

Let me know in the comments below if you have other banking concerns or inquiries about managing your transactions in QBO. I'm just around to help. Take care always.