Turn off indexing, commit the changes and then turn on indexing.
1) In InTrust Manager go to Data Stores
2) Right click on the your repository and go to properties.
3) On the Indexing tab uncheck Enabled
4) Commit the changes (blue check mark)
5) Go back to the Repository properties and enable the Indexing again and commit the changes.
NOTE: For very large repositories this will take some time for it to catch up on indexing, but when opening the repository viewer it will no longer show that it isn't indexed.
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