You should update your sitemap and send it to search engines, that is an important first step.
Additional to the sitemap, if you moved those resources to a new location in the new structure, then use 301 redirections. If they just disappeared, whatever the reason, then use 410 status to inform crawlers that they are not available anymore.
There is no need to touch the robots.txt file as you mention since that would be incorrect regarding the real structure of the site.