After playing with the api today I see that the vCenter ID is also tracked. I missed that somehow. Running this command:
curl -X POST -b ./tmpcookie --user admin http://myserver/HttpPostAdapter/OpenAPIServlet -d "action=lookupResource&resourceName="myresource"" -k
Yielded this response:
resourceName=myresource&adapterKindKey=VMWARE&resourceKindKey=VirtualMachine&identifiers=VMEntityName::myresource::false$$VMEntityObjectID::vm-123$$VMEntityVCID::OURUNIQUEID
So it looks like VMEntityObjectID + VMEntityVCID is what I need to make a unique match. Now we can confidently link these items together.