QuickBooks Online payment recording can fail when account mixed with parents and subs
There is a known issue that affects only the QuickBooks Online integration when applying payments. The recording can fail when the invoices being paid have mixed customer parent or sub. This works fine with QuickBooks Desktop. Applying payments (even for a sub customer) to mixed customers is not permitted with QuickBooks Online.
The solution is to not allow this within the payment user interface. The proper way to handle this is to render the payment screen so that the user can only apply payments to multiple invoices when they belong to the same customer (same level). As this does not apply to QuickBooks Desktop, this will not be enforced with those integrations.