Maybe This Time — Robert E. Dunn

"So far they haven't found anything, except a way to stop the spread," Tony explained. "What happens if you don't stop it?"
"There will be no building there at all and then no land at all. Then the nearby buildings and land will disappear, then all of Binghamton, then all of New York, Pennsylvania and then"

Nine-year-old Aaron Fisher is exploring the forest near his home when he stubs his toe on a rock in the middle of a bare spot in the woods. His toe begins to slowly disappear bit by bit. His doctor finds a way to stop the disintegration of flesh and bone, but his research eventually involves top scientists from all corners of the world. They fail to find the cause of the disintegration of the toe, and the area surrounding the forest of New York, Pennsylvania, and possibly the world will be gone, too.
When an unexpected visitor reveals the cause and the solution, it is then up to science to convince leaders of religion and governments that God is as real as the universe and that he has given up on us. Will this be the end?