How do I create a secondary version of the_content

You’re overcomplicating things. If you want the_content() to behave as it usually does, then don’t change it via filter or similar.

Just create your new custom function, eg like so (could be placed in your functions.php or if you’re in a plugin somewhere there)

function replaced_content() {
    $content = get_the_content();
    // $content = str_replace ...
    print $content;
}

Then you can use it just like any other function

<div class="main-content"><?php the_content(); ?></div>

<div class="another-content"><?php replaced_content(); ?></div>