Samadhi Cushions unfortunately has closed, so I can no longer get instructions or filling from them to refill or recharge my zafu, but it turns out the insides are easily exposed with no tools so I can re-stuff them.
Once I took off the zipper cover, I groped around the folds in the cloth on the side. Eventually I found find a spot where the fabric case opens up. There's a flap of fabric in front covering the hole. The hole itself is a slit in the case through which I can reach the stuffing. In theory, I'd just have to order some kapok fiber on Amazon and stuff more of it up in that space.
[Confusingly enough, I thought when I measured today the loft seemed higher than I remembered. I remembered it reaching 4.5 inches after a 30 minute sit whereas I needed it to be at 5 inches. Today it's at 6 inches. So maybe I don't need to stuff it after all. But then why was I having problems? That's a different thing to check on.]
Once I found the slit, I found it hard to get the pillow back into the case. I suspect getting the pillow back in the case is harder than re-stuffing the pillow would be.