Similar to removing resources, if a facility was given to an acid it cannot be removed.
You will have to remove the facility from any acids that have been given access to it.
To find the acids granted access to the facility issue:
TSS WHOHAS FACILITY(facility name)
Remove the acids access to the facility:
TSS REMOVE(acid) FAC(facility name)
Once all of the acids are removed from the facility the TSS MODIFY(FAC(ALL)) will no longer display the facility after the next recycle or IPL.