I have redirected my domain with a RewriteRule on the htaccess file on another domain's index page. Does this method affect the FTP connection?
If yes how can I bypass that?
.htaccess is Apache web server configuration file. The Apache is HTTP server. It has nothing to do with FTP.
.htaccess does not affect the FTP.
Even if it had impact, the FTP protocol does not support a redirection anyway.