Your scenario seems implies that the original charge and the chargeback happen in different tax years, because if it was the same tax year, the chargeback would just invalidate the original charge.

In the cross-tax-year case, you pay the chargeback from the historical profits you have been booking from the LLC and book it as a business expense in the current tax year.

If you are running an LLC with zero cash backup to handle such situations, there could be a problem with the business model.