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That is correct -you cannot modify credit applications as part of an existing payment

Only for understand it better. So if a user wrongly select a credit invoice to apply to invoice when creating a payment and he just figure it out after the save, is him supposed to delete the payment and create it again?

If you select a bad credit invoice to apply to the invoice - you edit the credit memo and unapply it from the invoice.

Then you can modify the payment to the correct amount, or delete it and do it again.

What if the credit is in a closed period?

involves marking the "allow non/GL changes"

though honestly I'd be half tempted to create a new invoice/vendor bill first.