Q:

Has any place exhumed more dead bodies than San Francisco?

San Francisco's cemeteries of the 1800s relied upon burial fees for maintenance, and so fell into disrepair when they filled up. Simultaneously, land became more expensive and public health fears proliferated, and in 1913 or 1914 the city ordered the cemeteries out, with two exceptions. Over a couple of decades, the remains of 130,000 or 150,000 people were moved to Colma (the U.S. has little or no tradition of grave reuse). Of course, the project did miss some graves.
Has any other project ever moved so many human remains? I've found this quite a challenge to look up. Most mass exhumations are of unitary mass graves, not removals of whole cemeteries. 

A:

The Catacombs of Paris contain the remains of more than 6 million people, and much like the San Francisco situation the catacombs were established to alleviate overflowing cemeteries throughout Paris. These catacombs were built using defunct mines and quarries spread out underneath Paris, and millions of remains were moved there from cemeteries across the city.
Of particular note was the Holy Innocents' Cemetery which, over the course of 600 years of operation, accumulated the remains of around 2 million people, all of which were moved to the new ossuary after the bones began overflowing into adjacent basements. 

A:

Singapore: over 250,000 individual graves exhumed, and more will follow.

Reasonably accurate estimates of the number of individual graves exhumed can be established for Singapore where more than 20 cemeteries have been cleared.

By 1985, 21 cemeteries had been cleared, and an approximate 120,000
  graves had been exhumed by the Housing Development Board.

Many of these were from Bishan (Peck San Theng). The Chinese Peck San Theng cemetery, which was also the scene of a battle in 1942, was closed in 1973 and exhumations began in 1982. Most of the graves were moved to a columbarium but it seems not all were found.

Peck San Theng Columbarium. "Front view of the columbarium, which holds the remains of 100 000 people." Image & text source: rafflespress.com
Before exhumations started in 2001, Bidadari cemetery used to have approximately 147,000 graves. According to Ghetto Singapore,

The first burial at Bidadari Cemetery happened on 15 December 1907. By the time the last burial was carried out in 1972, the cemetery was filled to capacity with approximately 147,000 graves.
Bidadari Cemetery was closed for burials in 1972, and the graves were
  exhumed in 2001 to make way for future housing and the development of
  the North-East MRT Line. Many use the park as a place of recreation
  today.

"Bidadari Cemetery in 1996. Image courtesy of National Archives of Singapore (NAS)." Text & image source: Ghetto Singapore
However, the actual number of graves exhumed seems to have been 128,000:

Between 2001 and 2006, all known graves, consisting of 58,000
  Christian and 68,000 Muslim graves, were exhumed. The majority of the
  Christian graves were unclaimed. The remains of Muslims were reburied
  at the Pusara Abidi Cemetery in Choa Chu Kang,8 while unclaimed
  Christians remains were cremated, and their ashes scattered at sea
  between 24 and 29 March 2008.

Also, in 2017, the exhumation of 80,500 graves the Choa Chu Kang cemetery began.

