While All Orders tries to ensure each document being posted to Quickbooks only goes over a single time there are instances where duplicates can happen. The most common one is when All Orders sends a new document to Quickbooks but never gets a valid response back letting it know it made it in successfully even though that may in fact be the case.
To help prevent duplicates log into All Orders as the admin and from the Company menu select Preferences. In the Quickbooks Synchronization preferences under the Advanced tab there is an option to not warn users about duplicates. Make sure this setting is turned off to get warned before duplicates can happen.
In the event that you get warned about a duplicate there will be two options for dealing with them.
Option 1 is to delete the document in Quickbooks and try to sync or send over the document again. This time there should be no warning and the document should post over.
Option 2 is to mark the document in All Orders as NC Only. This is telling All Orders that a copy of this document already exists in Quickbooks and it no longer needs to try and get posted into Quickbooks.