If you have signed into QuickBooks Online to authorize, but your issue is still not fixed, you probably have QuickBooks Online installed on two stores. The integration of one Shopify store to one QuickBooks Online account is what we support. You can't have multiple stores connected to QuickBooks Online; the authentication will override each other.
As a workaround, you could disconnect one store, export the connected store, then disconnect and repeat. This workaround is quite time-consuming, but it is the only option at this time.