You can deactivate search-based alerts.
When you reset the index and recrawl content, search-based alerts treat all results as new whether or not they were changed since the last crawl. This can cause users to receive unnecessary alerts.
When you reset the index and recrawl content, it is recommended that alerts be disabled until a full update is completed.
On the Search Administration page, under System Status, next to Search alerts status, click Disable.
Once the update is complete, enable the search-based alerts by clicking Enable.