Hi Maity,
Any type of TDS manual adjustments will not reflect in TDS tables and it is going to be big issue while generating monthly reports / year-end reports.
By doing the below steps you can resolve your issue:
1) Reverse manually adjusted TDS entry.
2) Create one more Vendor advance payment using transaction F-48, in the advance deduct necessary TDS amount and debit to vendor.
3) Using manual journal entry, cancel vendor payment (Debit Bank and Credit Vendor).
Try this and let us know if you need assistance.
Thanks & Regards,
Sarma Bhamidipati