I have slightly similar experience. When I was a teenager, I had a random flu shortly before two flights abroad. I didn't feel that sick anymore, but apparently my ears were still badly blocked. On descent my ears would hurt like hell, and I was half-deaf for rest of the day. That was more than ten years ago, and since then I've suffered from moderate tinnitus.

I too got used to it, but I would really advice people to avoid flying sick if they can help it (or at least use some meds to unblock your ears while doing it).