The Affordable Care Act does not determine the exact policies an employer can apply in their use of an HRA (it impacts HRA usage in some other ways but not in the context you are concerned with). You didn’t provide any details as to how your employer has structured their HRA and whether your employer’s health plan is fully-insured or self-funded. It may be that your employer has structured their plan design so that HRA dollars are used first, this is an allowed arrangement. It may even be that the HRA is limited to particular services.
If, as you seem to describe, you have a separate card from the drug manufacturer that covers a substantial portion of the prescription’s cost you may want to discuss with your pharmacist what your out-of-pocket cost for the prescription would be using the discount card and not filing it as a claim against your employer’s health insurance plan. You might even want to shop around as prescription costs can vary significantly from one pharmacy provider to the next. If the discount card is covering most of the cost of your prescription and you are wanting to conserve your HRA dollars then paying out of pocket may be the best way to accomplish that.
Also, I would recommend that you have your employer or your employer’s human resources person explain to you in more detail how they have their HRA arrangement set up so that you can most effectively use it going forward.