Hi There,
The reason this conflict typically occurs is because the Line Items on transactions created from other transactions (ie Sales Order > Invoice) are not in the same order.
For example, I create a Sales Order with line items (A), (B), and (C) in that order. I then create an Invoice directly from this Sales Order, but once it syncs I go in and change the order of the Line items on this Invoice to (B), (A), (C). QuickBooks doesnt like this one bit.
That being said, there are a number of different reasons why this conflict can occur and this is just the most common of the reasons. I would recommend in your case to give our support line a call at 1.888.925.6238 x 2 and have a supprt rep take a look at this one for you.
Thanks!
Regards,
Ben