You may try the following steps to rebuild the index. 1. Stop Portal for ArcGIS Service. 2. Navigate to C:\arcgisportal\index\nodes\0\indices (depending on your portal folder) 3. Delete all the folders in indices 4. Navigate to C:\Program Files\ArcGIS\Portal\framework\template\empty_index.zip (depends on your installation folder) 5. Extract the folders into C:\arcgisportal\index\nodes\0\indices 6. Start Portal for ArcGIS. 7. Navigate to https://<fqdn>/<webadaptorname>/portaladmin/system/indexer/reindex 8. Perform a full reindex. I followed the steps above to resolve mine. Hope it helps.
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