Load the payments with invoice numbers in the payments interface table or custom table.  Use a custom program to determine the appropriate amount to apply and insert/update that amount into the applied_amount field in the payments interface.

AutoInvoice Error:Too many rows returned

The most common cause of this is that RA_INTERFACE_LINES table have several rows in which have identical combinations of segments in the line transaction flexfield attributes INTERFACE_LINE_ATTRIBUTE1 to 15. The solution is make them unique.

Adding new segment in Chart of Accounts and Autoaccounting

If you add one more segment to your chart of account, it doesn't show up automatically in AutoAccounting setup. You need to
delete all the date from RA_ACCOUNT_DEFAULTS_ALL and RA_ACCOUNT_DEFAULT_SEGMENTS tables and then do need to setup AutoAccouting again. The new segment will appear in the pick list when you will set AutoAccounting again.

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