As report­ed in the Philadel­phia Inquirer:

How many skele­tons might remain buried? Pos­si­bly thou­sands, accord­ing to archae­ol­o­gists, but no one knows. His­tor­i­cal maps are unclear on the ceme­ter­ies’ bound­aries, but numer­ous his­to­ries por­tray the grounds as used first by Quak­ers and then by the poor, whose num­bers increased along with the size of the city. 

They quote the Philadel­phia Year­ly Meet­ing gen­er­al sec­re­tary, who had heard noth­ing about this. The arti­cle also cites a 1880s arti­cle in Friends Intel­li­gencer, the pre­de­ces­sor to Friends Jour­nal.

https://​www​.philly​.com/​a​r​t​s​/​s​c​h​u​y​l​k​i​l​l​-​y​a​r​d​s​-​q​u​a​k​e​r​-​c​e​m​e​t​e​r​i​e​s​-​p​h​i​l​a​d​e​l​p​h​i​a​-​h​i​s​t​o​r​y​-​b​r​a​n​d​y​w​i​n​e​-​d​r​e​x​e​l​-​2​0​1​9​0​5​0​2​.​h​tml