core_url_rewrite table error Magento professional needed

Hi all, I have magento store 1.7.0.2 CE I manage more then 4000 products and use Magmi Mass Importer for new product updates etc. I have more than 3000 rewrites in htaccess. Seems like every time i upload new products it corrups my core_url_rewrite table , my home page returns 404 error This is how my host server fixes that for me; "1) Backup your DB 2) Go into mysql and select your magento database. 3) truncate the core_url_rewrite table 4) Run the indexer located in /home/markizas/public_html/shell so : php [login to view URL] reindexall - if you are in that directory the command takes a bit of time to run, for your site it was about 30 seconds." I have to use importer I need a fix for this problem Thank you!