It has been found when a Credit Memo is applied to an invoice in QBO, and a part payment is applied, the payment applied in ConnectWise is incorrect and is applying the full amount. The resolve the issue Wise-Sync created a new function in v4.3.6 where payments apply the correct payment amount in ConnectWise.
When you apply a Credit Memo, you should see that the payment will be applied, and this will be excluded from the sync (payment amount) when synced back to ConnectWise. This is the process to ensure that when you apply the Credit Memo in ConnectWise, it won't create a double entry of the amount from QuickBooks Online and the amount is from the Credit Memo in ConnectWise being applied.
If you have Credit Memo's and Payments applied together, then the issue will still be that the payment amount contains the credit memo, and may result in the payment syncing each time that you sync payments in Wise-Sync.
To ensure the correct amounts are applied in ConnectWise, you will need to ensure that each Credit Memo is applies on it's own, not mixed with other payments, or with multiple Credit Memo's together in a single payment.
5 Payments Applied
Apply Credit to a single invoice
Invoices Created and Synced to QuickBooks Online
Invoices #400 showing all payments applied