This article is for extension version 126.96.36.199 and above
Make sure that you have full database backup before doing anything. Check if backup was created properly.
If you prefer to do it via admin - read here
Then connect to your server via SSH and navigate to magento root folder (below step is only possible when your index is not currupted - otherwise delete index folder completely)
php shell/lucene-tool.php --mark_unprocessed 1
You can confirm in Self-Diagnozing page (In admin -> System -> BlastLucene diagnostics) that number of processed products for store with ID 1 will be zero now.
Now deleteall documents in index for store ID 1
php shell/lucene-tool.php --removeall 1
Above step can be achieved by removing folder var/indexer/STOREID (when you index is corrupted or not accessible via php)
You can confirm in Self-Diagnozing page that number of indexed products for store ID 1 will be zero .
Now go to extension admin screen and enable "Indexing only new products"
Once done you can reindex via SSH (https://php4u.zendesk.com/entries/20254616-How-to-rebuild-lucene-index-from-command-line-SSH-) or Web browser (https://php4u.zendesk.com/entries/20260247-How-to-rebuild-Lucene-index-via-admin-screen-)
You can disable extension on frontend in admin screen for time when you run indexing