QuickBooks has recently introduced a new message which is displayed depending on your Sales settings.
This prevents Syngency from updating an invoice or bill, if a payment has already been added to it.
If you want to override this behaviour, follow these steps:
Click the Settings icon in the top-right corner of your QuickBooks screen
Under Company Settings > Sales > Sales Form Content, find the checkbox labelled Deposit.
Make sure the Deposit checkbox is checked.
Now Syngency is able to update invoices and bills that have already had payments assigned to them.