After I got my car repaired, I noticed it started to make funny noises
which it had not made before/ which I had not heard before.
got my car repaired, I noticed it started to make funny noises which
it has not made before / which I have not heard before.
The function of tense shifts in situations like this is either to establish or to corroborate a Reference Time. If other temporal elements of the sentence already do this, then all of the responsibility no longer rests on the shoulders of the verb tense. The verb tense can corroborate--if corroboration is deemed necessary for the sake of clarity. Speech is communication, after all, not a programming language.
Since other temporal elements of the sentence establish the reference time ("After I got my car fixed it started to make funny noises..." ) you are free to say either ...which it had not made before or ...which it has not made before.
Are there situations where you would choose the one over the other? Yes.
If you are speaking to the mechanic who made the repair yesterday, you might say "funny noises which it has not made before" to emphasize the fact that from the day you bought the car up until the present repair, it has never made these funny sounds.
If you are suing the mechanic in a court of law for ruining your car, and the repair occurred eighteen months ago, and your case has only now come before the court, then you need to refer to two times in the past, and you would probably say to the judge, "the car made funny noises which it had not made before the repair."