Portal search collections gets corrupted.

Generally Portal search collections may gets corrupted in following scenarios

Scenario 1.
This happens after applying fixpack or ifix.

Scenario 2.
This happens after the abnormal shoutdown of the remote search server or the local search server, depending on how you have configured the search service.
Resolving the problem  
Scenario 1.
The index structure of Portal search is not backward compatible between the different product versions. For this reason you need to preserve your search collections before you upgrade your Portal server. To preserve search collections, export the collections prior to upgrade and then import them back using the "Manage Search" admin portlet.
Scenario 2.
If, the crawler is running and the remote search server or the local search server(depending on how you have configured the search service) terminates unexpectedly then it is normal to see the search collections disappear or get corrupted. The only way to prevent this is to make sure the servers are shutdown gracefully. For a quick recovery, keep backup copies of all the collections, by exporting them using the "Manage Search" admin portlet. This way you can restore the collections after the failure by importing them back into a new collection.
You should also delete the faulty collections before creating a new one.

For IBM® WebSphere® Portal version 6.0 and 6.1
Faulty Index cleanup portlet is integrated into 6.0.0.x and 6.1 to "Manage Search" admin portlet Go to:
Manage Search -> Default Portal Search Service

You will see a link at the bottom "Manage Faulty Collections" only if there are any faulty/corrupted collections

NOTE: In some cases you may require to delete the collections physically from the hard disk first and then use the faulty collection portlet/functionality to completely remove them from the machine. This may require portal restart

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