Indexing runs all the time. The role of the Indexing Service can be summarized as follows:
On instruction from the Storage Service, the Indexing Service indexes items as they are archived. It uses the AltaVista� Search technology to create and store indexing data about each item. There is one index for each archive.
The locations of index files are specified in the Indexing Service properties.
If an index is out of date, the Indexing Service automatically updates the index.
In response to requests from the Enterprise Vault web access components, the Indexing Service searches these indexes and returns information about the archived items that match the search criteria.
You want it to stay running.