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When you buy something and don't have enough funds in your bank account then paypal will put your account into negative and then TRY AGAIN a few days later, if that again fails then they will try your back up card if you have one linked.
However if in the meantime you transfer funds 'as well' then whichever payment reaches your paypal balance first will clear the neg balance and the second one will be credited to your balance and you can withdraw it back to your bank account if you wish to.
So as you know paypal have successfully got the money from your bank account then do nothing until that payment hits your balance to resolve the neg balance. (can be up to about a week).