There was a fire in the early 1800s ... when they rebuilt the place, they were apparently in a bit of a hurry. They filled in the crypt (dumb, but they didn't ask me) and built the main altar over it.
It does seem bizzare to me that if they felt it was the final resting place of St Paul they wouldn't have immeadiatly set to work trying to restore it (its not like Catholics suddenly forgot they generally hold relics of Saints in high esteem...) Still (as an Orthodox Christian) I'm glad to see them being recovered now.