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Solution: Rebate can be entered using Credit Note document and Output VAT transaction for the tax.
1. Create Credit Note with the type - Mutual Settlement Adjustment, Expense GL account select corresponding account that should be credited:
See also 3.2.7. Credit Notes
In Documents tab, specify the sales invoice you want to allocate the amount to (i.e. close receivable balance). Put the check mark for Advance column, so Credit note can be adjusted with future invoices:
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The Credit Note will be shown in Company's Statement under Advances Received:
2. Create Output VAT Transaction to register Tax for rebate:
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