It no Snapshots are shown in the Snapshot Manager with the "Show AutoProtect snapshots" check box checked then the Snapshot is orphaned and the easiest way I normally use to resolve this if I want the contents of the orphaned snapshot to be part of the base disk is with the VM's tab closed in the VMware Workstation GUI I simply delete the .vmsd file and then open the VM's tab in the VMware Workstation GUI and then take and immediately delete a Snapshot from the Snapshot Manager. This will force the orphaned snapshot to be merged with the parent disk. Then to clean up I again delete the .vmsd file and any orphaned .vmsn and .vmem files.
Note: Before proceeding ensure you have a proper backup of the VM in case you accidentally mess something up.