Try to deploy some RR pair from eclipse plug-in to the existing VS didn't update the VSI.
When Customer created VS and deployed to the VSE, there is no VSname.vts file available in the Project/Data folder which caused the issue.
Release : 10.5
Component : CA Service Virtualization
Creating a VS should create a VSname.vts file in the Project Data folder. Then deploy that VS to VSE and then try adding RR pairs to the VS from Eclipse plug-in should work.
The available patches from Eclipse-Plugin_Jars.zip should be applied for the functionality to work. The file Steps_To_Apply_Patch.txt will provide information on applying the patches.
Please open a new case and refer DE430201 to get the patches.