Hi The_Interphaser,
I get how having an open invoice can throw a wrench into your invoicing flow.
Typically, reversing a transaction just flips it to a negative value to balance things out. But if you need to remove the invoice altogether, you might have to delete it. Check out these help articles 'Reversing a Transaction' and 'Deleting a Transaction' for more details.
Depending on what you need, you can tweak your preferences to allow reversals or deletions of transactions.
Feel free to let us know if you require any other assistance.
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Thanks,
Genreve