You use the 
Change
Payment Tolerance batch job to change either or both the
maximum payment tolerance and the payment tolerance percentage and
filter by currency. If there are open customer and vendor ledger
entries, the program will ask if you want to change all open
entries that are not blocked and the entries will be updated
accordingly.
Click OK to start the batch job. Fill in the relevant fields as follows:
All Currencies: Insert a check mark if you want to change the tolerance setup for both local and all foreign currencies.
Currency Code: Enter the code of the currency for which you want to change the tolerance setup.
Payment Tolerance %: Enter the percentage by which the payment or refund is allowed to be less than the amount on the invoice or credit memo.
Max. Payment Tolerance: Enter the maximum allowed amount that the payment or refund can differ from the amount on the invoice or credit memo.