Just to understand where you are at. You have 1 vCenter endpoint already created using the proxy agent you initially installed. Is the name on that proxy agent vCenter? Then you needed to add another vCenter. This is the one you aren't seeing inventory for. So you installed another proxy agent and called it...vCenter2? When initial installed did you do a distributed installation or complete installation of IAAS components?
vRA will not get rid of clusters it has seen even if they are deleted or renamed . Take a look at this KB Deleting an endpoint in vRealize Automation fails with the error: This endpoint is being used by # compute resources and # storage paths and cannot be deleted for a procedure to remove inactive hosts from vRA.
Thanks for that, I didnt realise a second proxy agent was required for the new vcenter. and that article is really useful