If during invoice posting, the user has decided to change the method of payment defined in vendor master data by another method of payment, the method of payment defined during invoice registration should be initialized during vendor payment journal. This works correctly when creating payments through vendor payment proposal, but unfortunately does not work when the user settles manually the invoice with the payment.
Current Microsoft's feedback Details for issue 663847 (dynamics.com)
Settling invoices on a vendor payment line will not change its method of payments, as its method of payment may have already changed and set manually by the user, and one payment line may settle multiple invoices with different method of payments. This is different from the payment proposal. The difference is that, during the creation of the payment proposal, there is no payment line generated yet. However, when user tries to settle invoices for a payment line, the payment line is already created and has a method of payments on it.