There are a few possibilities here. During the earlier stages of adrenal fatigue the adrenals are actually over-producing cortisol-- usually to compensate for, and in response to, stress on the body, like hypothyroidism. If we are already flooded with extra cortisol additional amounts can be counter productive. Excess cortisol will also cause high reverse T3 levels and these will clog up the T3 receptors and make us more hypo-- not to mention give us a lot of nasty symptoms.
Later when adrenals have been stressed for a long time they start to falter and produce less cortisol than we need and we get more hypo still.
Also when we go on replacement therapy of hydrocortisone for adrenal fatigue we start at a very low dose and slowly titrate up and don't go above a physiologic dose. Starting on a high-dose Medrol dose pack could have been the wrong move here and isn't how we treat our AF.
I also think the idea that the stress of the surgery whacking out the thyroid is a good one too.