ESRI support team was able to fix the issue using following steps
-In the arcgisportal/content/items folder, there was a kml folder, removed that folder from folder
-Ran the following workflow:
1.Stop Portal for ArcGIS service
2.Rename Content, db, and index folders inside C:/acrgisportal to to Content_old, db_old, index_old
3. Copy the Content, db and index folders from C:\arcgisportal\upgrade-backup\10.6 and place them into C:\arcgisportal
4. Clear browser cache and close browse
Run the setup again
-Site was successfully upgraded