Welcome to the Community,
Only the "ScratchConfig.ConfiguredScratchLocation" can be modified. "ScratchConfig.CurrentScratchLocation" will show the reconfigured location after the reboot.
Please note that it may also be necessary to reconfigure "Syslog.global.logDir" (see https://kb.vmware.com/kb/2003322) if it points to a location on the datsatore that you want to delete.
As a side note: Although it may be possible to create multiple VMFS datastores on a single disk/LUN, please remember that only a single one is supported.
André