This occurs for no reason sometimes. However, I have found this mostly happen when NT blue screens.
When the index gets corrupt you need to stop the service, delete the old index file and restart the software.
You can use the MMC to do this.
Also, I have found that you can just stop the "Content Index" service, wait a few seconds and restart it. That seems to cause the Index Server to reindex all the files.
Note: To build the index takes a while. Even though the service is restarting, the server is building the index. You can search while it is still building the index, but you can get incomplete returns until it is complete.
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