You need edit a .htaccess file under respective "public" folder of a application if you are running multiple ROR applications under your account. It wont conflict but you need to make sure to terminate previously running dispatch.fcgi if there any for that application and then deploy it again. Just like a restart.
Do not use a generalized .htaccess file for all applications.
A good news for you is, mod_proxy has been enabled on server.
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