Tracking Redirects

I have a moderate amount of traffic mostly generated by genealogical search engine links. I am testing a new site in a directory and using a mod_rewrite redirect which works fine. I added to my .htaccess:
"RewriteCond %{REQUEST_URI} !^/webtrees/
RewriteRule ^(.*)$ /webtrees/$1
Now my Piwik report has dropped from 70/day to zero. I had my website set for and added the site and set my report for “All websites Dashboard” but still show zero visitors. Am I doing something wrong? Thanks.