Strip shortcode tags for inactive shortcodes and leave content as is.

wp-strip-inactive-shortcodes.php

<?php
/**
 * Hook
 */
add_filter( 'the_content', 'remove_inactive_shortcodes' );
/**
 * Remove inactive shortcodes
 *
 * Make sure inactive shortcodes don't leave their junk in the content.
 * We are striping their tags, leaving content as is. This function is attached to
 * 'the_content' filter hook.
 *
 * @global $shortcode_tags 	Associative array of all active shortcodes.
 * @link https://wordpress.org/support/topic/stripping-shortcodes-keeping-the-content/#post-2704758
 * 
 * @param string $content  Content to be filtered
 * @return string          Returns filtered content
 */
function remove_inactive_shortcodes( $content ) {
	global $shortcode_tags;

	$keys          = array_keys( $shortcode_tags );
	$exclude_codes = implode( '|', $keys );
	$the_content   = get_the_content();

	// strip all shortcodes except $exclude_codes and keep all content
	$the_content = preg_replace( "~(?:\[/?)(?!(?:$exclude_codes))[^/\]]+/?\]~s", '', $the_content );

	$content = $the_content;
	return $content;
}