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Hello there, @info837.
Currently, we're unable to link square invoices and QuickBooks Online (QBO) invoices. Once you connect your Square account, QBO will only download your Square transactions.
To learn more about sync Square to QBO, do check this article for more details: Sync Square with QuickBooks Online.
Also, I'll take note of this feature request on your behalf and pass it to our product developers. They are always on the look to improve our products that suit the need of our customers.
To know what our developers are up to, I suggest checking our QuickBooks Blog page for the latest news and updates.
You might also want to check this article that can guide you reconciling your accounts in QBO: Reconcile an account in QuickBooks Online.
You're always welcome to post here anytime you need help. I'd be happy to work with you. Have a great day and always stay healthy!