You are free to take the matter up with Quest's billing office. In fact you should. You also can, and should, contact your insurance carrier and ask them if, when a non-network doctor sends you to an in-network lab, are the lab charges payable under the policy.
But the thing is, the doctor's office is not the one that negotiates rates for the patient. That negotiation is done by the insurance carrier, not the doctor's office.
What matters here is whether lab charges associated with a non-covered doctor visit are or are not covered under the your specific health insurance plan. Only your insurance carrier can say whether they are or not. It's unlikely, but I'm not going to say it's impossible.
If lab charges associated with a non-covered visit ARE covered, your insurance carrier will be able to help you sort this out. If that is the case, the negotiated rate that your insurance carrier (not the doctor - as I said above, the doctor's office is not the one that negotiates rates for patients with the lab) most likely would be in force, though your insurance carrier will have to say for sure and also say what that rate is. It would be best if you could come up with some form of proof of payment; either your cancelled check, your bank statement showing the payment, or a receipt. I am not even remotely questioning you when you say you pre-paid, but if that pre-payment did not get posted properly, you are going to have to prove that you've already paid. Mistakes do happen; records of payment do get lost, and if Quest does not have a record of the payment (even if that means their records are wrong) it is in your best interests to show what payment has already been made and not rely on Quest to have that record. BTW, this assumes that Quest is an in-network lab on your insurance. If Quest is not an in-network lab on your plan, see below.
If lab charges associated with a non-covered visit are NOT covered, which is what I suspect you will find to be the case (though I do hope for your sake that I am wrong) then the rates the carrier negotiated are out the window and Quest can charge you whatever their normal rates are, minus what you can prove you have already paid. This is also the case if Quest is not a covered lab on your plan.
In my experience (and we are talking close to 35 years worth here) Quest is a reputable lab and honest, but they do occasionally have problems with their billing. They cannot keep adding on new charges but from what you've said I don't think that's what they're doing; I think that they've lost or mislaid the record of your prior payment and are charging you the full amount again because your insurance carrier didn't pay. I have no doubt that if you can show that evidence of prior payment you will be credited with that. But whether or not you are entitled to the rate negotiated by your insurance carrier remains to be seen.

