I don't know why it happens, Becky, but it does happen, especially with black swallowtails. I don't think any of the black swallowtails I raised earlier this year have emerged yet. I've had many black swallowtails that took a year to emerge, and my all-time record is 18 months!!
I raised a lot of pipevine swallowtails earlier, then didn't for a while, because there were no more pipevine leaves. About two-thirds of them emerged, but there are still quite a few in their chrysalis. Their color looks good, as does the color of the black swallowtail chrysalides, so I'm figuring they'll emerge eventually. Unless a chrysalis is very dark, sooty black, it's likely alive and healthy.