It is possible to integrate VIN in linked mode VC environment, if you deploy VIN at each of the VCs.
For more information, please refer 'Setting Up Infrastructure Navigator' in VIN's Admin Guide.
I hope it works for you,
Even in liked mode, each VIN instance is displaying VMs from second vCenter Server as external VMs and stops discovering any further dependencies. I didn't find any reference to specific instructions for VIN setup in linked mode. Can you please provide link to the section you referred to? thanks
In linked mode, VIN shows the other VC's VMs as external IPs by design.
VIN supports linked mode in a sense it discovers the environment of the particular VC although there are two environments (i.e. two VM lists) connected.
In addition, in VIN's window settings you can use the drop box and select which VC to discover.
If you experience any discovering issues, I suggest you to open a SR so our Support team can research the logs and refer it.