smog tube/h-pipe question

I'm putting in an offroad h-pipe in my stang and i WILL be removing my smog equipment later. I am wondering if it will be ok if I just leave the pipe that is supposed to connect to the h-pipe just hanging there, not connected to anything. Will there be any adverse affects? The reason I don't just hook it up is because I bought the H used and the smog tube has been previously welded shut.
Thanks
 
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