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QBOI does apply discounts set in the AyaNova workorder to the QB Online invoice generated from it via QBOI.

 

If you have applied a discount on a part record in an AyaNova workorder, that net price which is the AyaNova part price X the discount will be identified by QBOI

 

If the AyaNova net price (part price X discount) is different than that of your QB Online item price, QBOI will identify that there is a price problem that needs to be addressed and will identify it as due to a discount (i.e Price XX.XX discounted XX% on workorder)

 

See also:

Fix AyaNova part that has a different price that QBO price