Hello,
You have two options:
1) you create a payment mode in sales or purchase ledger called Mutual Settlements, and then you create sales ledger receipt for 50K and purchase ledger payment for 50K using the same payment mode that will then get debit and credit both 50K
2) you can also create a new GL Transaction, open flip E, and make first row type C for customer, and select outstanding sales invoice for 50K. Then on the second row you make row type S for supplier, and select outstanding purchase invoice for 50K and save. You can also select multiple sales or purchase invoices like that, and adjust debit or credit amounts to make sure that total debit equals to total credit. This GL Transaction then also makes both the sales and purchase invoices paid in the ledger
Using receipts and payments with Mutual Settlements payment mode is better option if you want to use payments journal and receipt journal reports and see how much has been settled in a period. If you use GL Transaction, then you cannot easily see any report to see what amounts have been settled like that. Just check with your customer if this reporting is needed at all, if not then GL Transaction is easier entry, and you could use Settlement object on all rows to pull a report in GL for Debtors account or Creditors account to see all settlements.
Hope this helps.
Kind regards,
Kaido