Tony, both "that" and "which" are correct there, because there's no comma (the relative clause is defining or restrictive).
If the clause is non-definining or non-restrictive (i.e. it is preceded by a comma), then only "which" can be used.
Perhaps you could find a way to avoid the repetition of "invoices," for example:
You applied a 25% discount on the overhead expenditure invoices that/which were not charged to ABC Pty Ltd.