The alternative to the reversal is to undo the bill you sent to the client, and correct the payment by deleting it, or editing and assigning the corrected portion to the current project. Next, enter a separate payment with the remainder to the other project. In this scenario, you would then need to re-generate the bill for the original project. The message is merely cautioning you that you won't be able to undo the bill afterwards. There is no ill effect if you know how you want it to be processed. The reversal and subsequent re-application of the payment to the other project will be accounted for properly in Quickbooks.
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