@vaibhav There shouldn’t be any negative impact that comes to mind. The receipt ledger entry rolls the line tax amounts in to the cost, and that typically goes in to an accrued account. And then the voucher debits the accrued amount, debits your tax account for the tax amount, and credits the voucher total to AP.
As far as the taxable amount getting zeroed out, that popup window just serves as a calculator/worksheet, and the taxable amount being zero there shouldn’t be an issue. The reason it goes to zero is because once you manually change the amount, you’re overriding the amounts that came over from the PO, and so it clears the taxable amount.