Tax Deduction at Source (TDS) is not yet supported by Advanced Payment. This is documented on SuiteAnswers ID 108406 India Localization SuiteTax Engine Limitations that TDS calculation does not support bill credit and vendor prepayment. There is currently an Enhancement filed for this logged under Enhancement #576519 – Ability to calculate Tax Deduction at Source (TDS) on Vendor Payment.
Reference – NetSuite ACS ticket 5594776