Thank you for the reply @ClaireSamanthaS 

Correct me if I'm wrong, but QBO is the one who makes and updates the Square Integration app correct?  Is the refresh for Square app going to be integrated again?  It seems like many of these issues could be resolved with a refresh option for that app.  It pulls in CC transactions perfectly fine, the issue seems to only occur with cash/check/other transactions. 

As for the editing of the invoice, on the Square side I have tried both ways to send and not to send the updated invoice to the customer to see if that would trigger any different outcome for those invoices, but it does not.