Was the questionnaire legal under HIPPA regulations? Was my employer in violation in issuing the form for completion?
Yes, the form was legal under HIPAA and no, the employer wasn't in violation.
Was my employer in violation of securing the form adequately?
There is nothing in your facts that indicates the employer failed to secure the form. You don't specify what their procedures were, just that you had no way of knowing certain things. However, this particular question is always a question of fact that has to be decided by whoever is receiving the complaint and is not something that is the same for every case.
If my insurer is refusing to provide the medications for which I believe I am entitled (and paying monthly for under the ACA), is my insurer liable in any way because of my employer's lax paperwork oversight policies?
Not that I can see. Again, you don't state what the employer was doing, you just state you don't know what they were doing. However, regardless of whether the employer failed to protect the information sufficiently under HIPAA that is a separate issue from whether the claim should be paid. If they are denying the medication based on an incorrect answer you made on the form then how the form was handled isn't an issue as to whether they should pay. The issue is whether it is a valid denial based on the answers you gave. There is no way I can know that particular answer but you can certainly file a complaint. Your first step would be to file an appeal through whatever process they have in that policy. The next step is to file a complaint either with the Department of Insurance in your state or hire a lawyer who will then send a demand letter and if no response will then file a lawsuit.