On a Microsoft SharePoint 2010 server that uses Microsoft FAST Search Server for SharePoint 2010, if you issue an index reset from a FAST Content Search Service Application (SSA) you may receive the following message:
You need to manually clear the content collection on the backend after you have reset all crawled content in this service application, and before starting any new crawls.
The content index has already been fed into a content collection on the FAST Search for SharePoint backend. You must clear the content from this specific content collection on the backend to ensure data remains in sync. To do this, use PowerShell commandlets. Load the Microsoft.FASTSearch.Powershell snap-in on a FAST Search Server 2010 server and use the command Clear-FASTSearchContentCollection. Note that this is irreversible. Ensure that you clear the same collection as used by this service application.
After you issue an index reset, you must use the Clear-FASTSearchContentCollection command in Windows PowerShell. This command removes all the content in the FAST Search Server content collection passed as a parameter to the command.
To avoid losing content from other sources, you should ensure that the FAST Content SSA previously reset was the only SSA using this collection. You must make sure that this SSA was the only source of content in this collection. The default collection name is 'sp', and the Content SSA can only have one collection name specified. Clearing the collection in this way is irreversible and will erase the index. If any FAST-specific connectors (Web Crawler, Database Connector, Lotus Notes, etc.) also made of use of the collection (e.g. 'sp'), their content would also be lost.
It is possible to use separate collections for these other connectors, to avoid this scenario when clearing the SharePoint crawled data only.