The "Transaction already exists - save anyway?" error occurs when another transaction of the same type has been saved using the same number.
To locate the other transaction:
Make a note of the transaction number (invoice number, check number, etc.) for the transaction you're trying to save.
Select the Magnifying glass in the Toolbar.
Select Advanced Search.
Select All transactions, Reference no, Contains and enter the number of the transactions that you are trying to save.
This will show which transaction is causing the error to appear. You can choose to renumber and resave the old transaction, give the new transaction a different number before saving it, or save the new transaction with the same number.