1. Stop all InTrust services on the server running index.
2. Backup IndexingRoot$ folder of the problem repository (optional)
3. Run the tool(attached) using the following command:
index_support_tool2.exe --repair --repository_path <repository path> --index_root_path <index root path>
If Indexingroot$ folder is located in the repository folder, there is no need to use --index_root_path parameter
4. After the tool completes the index repair, start the InTrust services.