TDS amount getting wrong reverse in f-54

Hi experts
As per my knowledge tds is deducting twice. At the time of advance payment and invoice booking. and tds amount whichever is lower is getting reverse in f-54. But in my present scenario tds which is deducted at the time of invoice booking is getting reverse instead of tds which is deducted at the time of advance payment and i also check the tds amount is lower than tds amount of invoice.
This scenario has been occurred for only one vendor, In case of other vendors,its looks correct.
Please advise me .
Thanks&regards
D Roy

hello sir
Thanks for your early response.
According to my present scenario,At the time of Advance
Advance to sub contractor Rs.50000---dr.
tds payable on sub contractor Rs.500--cr.
Invoice
vendor  Rs.100000---cr.
tds payable Rs.1000---cr.
in f-54 tds Rs.500 should get reverse but system reversing  tds Rs.1000
Please advise

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