There are two issues competing here.
One issue is the grammatical correctness of the phrase. The other is, communicating the thing you intend so as to get the correct business or financial outcome.
The grammar of the sentence is OK as it stands. Changing "had" to "has" would also be acceptable. That seems to be the specifics of your question.
As to the financial aspect, consider that "had not gone through" refers to things as they were from some point and backward in time. For example, some brief time after the first payment was made. It could be true that it "had not gone through" at the time, but went through some time later. Or has not yet gone through, but now that the buyer has alerted the seller of a pending windfall of cash, it will get processed.
Thus "had not" would refer to the time before some (not precisely defined) time into the past. And "has not" would refer to the time the statement was made and into the past. Each is reasonable from a grammar point of view. And would be understood unless the person listening was being malicious.
The financial concern is that the first payment is not processed at any time. From a financial point of view you might want to change it to "has not and will not go through." This covers all time.