If the second vcenter also has its own SSO installed on the same machine and the second SSO was installed in multisite mode (expected to be yes, since the primary goal is linked mode), you need a clean up of vmdrd of first SSO.
VMware support has specific utility to get that done, Please file a case to get support.
vCenter installation is not going to be a problem, each installation has an application user ID created with install date, this ID and certificate (which is expected to be unique for a fresh install, need to clear ssl folders from programdata if re-installing) are used to register vcenter to SSO.
So old entries are not going to be an issue for other components.
still from the webclient you can remove application users:
Log in to webclient with Administrator@vsphere.local to the first web client.
Under configuration Users and groups, Under Application users tab you can see all the registered application users.
To identify which one to remove
for vcenter check the file C:\Program Files\VMware\Infrastructure\VirtualCenter Server\ssoregtool\vssso.properties.
once you know the ID of working vcenter, you can remove the other ID.
Same for inventory service, the ID of inventory service can be found from C:\Program Files\VMware\Infrastructure\Inventory Service\conf\sso.ini
For webclient the files is C:\Program Files\VMware\Infrastructure\vSphereWebClient\SsoRegTool\sso_conf\solution.ini
vCenter and webclient has a solution user registration with sso, that need to be removed from command line. This is the KB for that: 2033238
again you can use the files mentioned above to identify the one to remove.