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What is the best way to recover from an accidental double-spend?

Came across an issue where I was given the message:

"Error: The transaction was rejected. This might happen if some of the coins in your wallet were already spent, such as if you used a copy of wallet.dat and coins were spent in the copy but not marked as spent here."

It appears that the 2nd amount was deducted from my total balance even though it still sits at 0/unconfirmed status days later even though the unconfirmed transaction has disappeared from the blockchain.

Any suggestions? I've also installed Python and tried running a script provided by someone else (within Windows 7) and cannot seem to get the script to run properly.

Any help is greatly appreciated.