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After upgrading Portal for ArcGIS, the web application templates are not listed in the default location but are instead set to the location of the previous version.
The default group to display the web application templates has been changed to a custom group.
Solution 1: Set the default location of the web application templates.
1. In Portal for ArcGIS, navigate to My Organization > Map > Web Application Templates.
2. Select Default.
Solution 2: Reindex to generate or update the indexes for content in Portal for ArcGIS.
1. Open the Portal Administrator directory, and log in with an account that has administrator privileges. The Portal Administrator directory URL format is 'https://portal.domain.com:7443/arcgis/portaladmin'.
2. Navigate to System > Indexer > Reindex.
3. Click the Mode drop-down list, and select Full. Leave all other settings to default.
4. Click Reindex.
Reindexing completes the Portal for ArcGIS upgrade process. The time it takes for reindexing to complete depends on the number of users and amount of content in Portal for ArcGIS. This process must not be interrupted. To monitor the indexing status, navigate to System > Indexer > Get Index Status. Refresh the page to get the latest results.