I need some clarification if anyone happens to know this:

OK on my hosting account I have 3 addon domains. My main site for the account is on my hosting server under /public_html/. The three addon domains are in subdirectories of the public_html folder , public_html/addon1/, public_html/addon2/, public_html/addon3/. Well I have a script on some of the pages in my main site that lets you search my site as well as a dynamic php sitemap. The problem is that sometimes these search within the subdirectories that the addon domains are in and have somehow caused a few of those pages to be indexed under my main site. (ie: Google shows results for http://www.mainwebsite.com/addon1/addon1index.html)

So I figured I could add a robots.txt file under my main domain (in the public_html folder) and disallow addon1 addon2 addon3. Will this cause any problems with getting my addon domains indexed under their correct domain names? It doesn't seem like they would, but I want to be sure. Should I include a robots.txt in all of their folders that doesnt disallow anything? I only ask because I added the robots.txt about 2 weeks ago and suddenly dropped off yahoo... not sure if this is why though.
thanks

Shouldn't cause a problem. The addons will apear to be unique sites to the search engine and completly unrelated to the main site as if they were all hosted seperatly. However, it may be better to use .htaccess to redirect /addon1 folder to the domain url for the addon rather than blocking it. That way real people will be redirected as well as SE spiders.