In June 2017 Kimberlee Moran, a forensic scientist at Rutgers University-Camden, stood in a pit at a construction site in downtown Philadelphia, just across from the Betsy Ross House.

The walls of the pit were shored up by diagonal pillars of dirt. They bristled with coffin wood — and human bones. But what she couldn’t see bothered Ms. Moran still more.

“Where’s all the stuff in the dirt that’s now missing?” she wondered.

With her were Anna Dhody, a forensic anthropologist at the city’s Mütter Museum, and Kimberly Morrell, an archaeologist with the engineering firm Aecom, hired to excavate the site.

They were standing in what once was the cemetery of the First Baptist Church of Philadelphia, founded in 1698. Historical records said the remains were supposed to have been relocated to another cemetery, Mount Moriah, back in 1860.