Why is conditionally loading a custom plugin’s code only on a specific custom post type causing the site content to disappear?

I realize you’ve already answered your issue. However, I think there is some additional explanation possible to give more clarity to the issue and the solution.

The issue is your lqdnotes_add_div() function. This is hooked to a filter – the_content.

In WordPress, any time you use a filter, your filter function must return a value for the item being filtered. This might be a string, array, or boolean. In this case, $content is a string, and a string must be returned.

Your filter function only returned a value if the post type was “lqdnotes”. In all other cases a null value was returned.

While you do need to return a value for $content, you do not need to do this with an else condition. In fact, it is a good standard practice to make sure there is at least a return value at the end of any filter function to provide for returning an unfiltered result if any of the function’s other conditions are not met.

function lqdnotes_add_div( $content ) {
    if ( get_post_type( get_the_ID() ) == 'lqdnotes' ) {
        $updated_content="<div id="message-notes" class="message-notes">" . $content . '</div>';
        return $updated_content;
    }
    return $content;
}
add_filter( 'the_content', 'lqdnotes_add_div' );