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If you funded the original Paypal payment to the seller with a debit card then it won't go back to your paypal balance.
Once marked as completed it will automatically go back to your bank account but takes up to a week to process through to the bank (Paypal say allow 30 days but I have never waited longer than a week for mine, the last one taking 4 days).
If both old and new cards belong to the same bank account then the refund should go through fine.