Wordpress: Automatically change URLs in the_content section

autoembed is hooked at the_content with priority 8 on wp-includes/class-wp-embed.php:39

Try to lower the priority of the the_content filter so that the URL replacement happens before the embed, something like this:

add_filter( 'the_content', function ( $content ) {    /*     * Here, we define the replacements for each site in the network.     * '1' = main blog     * '2' = site 2 in the network, and so on     *     * To add more sites, just add the key number '3', etc     */    $network_replacements = [        '1' => [            [ 'shop' => 'shop1.com', 'id' => '11111' ],            [ 'shop' => 'shop2.co.uk', 'id' => '11112' ],        ],        '2' => [            [ 'shop' => 'shop-x1.com', 'id' => '11413' ],            [ 'shop' => 'shop-x2.net', 'id' => '11212' ],        ]    ];    // Early bail: Current blog ID does not have replacements defined    if ( ! array_key_exists( get_current_blog_id(), $network_replacements ) ) {        return $content;    }    $replacements = $network_replacements[ get_current_blog_id() ];    return preg_replace_callback( '/"+(http|https)(\:\/\/\S*' . $replacements['shop'] . '\S*")/', function( $matches ) use ( $replacements ) {        foreach ( $replacements as $rule ) {            if ( strpos( $matches[0], $rule['shop'] ) !== false ) {                $raw_url = trim( $matches[0], '"' );                return '"https://www.network-x.com/click/' . $rule['id'] . 'lorem_lorem=' . rawurlencode( $raw_url ) . '"';            }        }    }, $content );}, 1, 1 );

This is not a copy and paste solution, but should get you going. You might need to tweak your "preg_replace_callback" code, but you said it was working so I just left it is it was.

If preventing the wp auto-embed works, then just add this line to your theme functions.php

remove_filter( 'the_content', array( $GLOBALS['wp_embed'], 'autoembed' ), 8 );

I wrote solution without test. Your code is hard to test without your site but I think that problem is with regex. Callback is hard to debugging. My version below.

First step, change your structure. I suspect that domains are unique. One dimensional array is more useful.

$domains =  array(            'shop1.com'=>'11111',               'shop2.co.uk'=>'11112',            'shop-x1.com'=>'11413',             'shop-x2.net'=>'11212',        );

Next:

$dangerouschars  = array(  '.'=>'\.',);function wpso_change_urls( $content ) {   global $domains,$dangerouschars;   foreach($domains as $domain=>$id){      $escapedDomain = str_replace(array_keys($dangerouschars),array_values($dangerouschars), $domain);     if (preg_match_all('/=\s*"(\s*https?:\/\/(www\.)?'.$escapedDomain.'[^"]+)\s*"\s+/mi', $content, $matches)){        // $matches[0] - ="https://example.com"        // $matches[1] - https://example.com        for($i = 0; $i<count($matches[0]); $i++){                $matchedUrl = $matches[1][$i];                $url = rawurlencode($matchedUrl);                //is very important to replace with ="..."                $content = str_replace($matches[0][$i], "=\"https://www.network-x.com/click/{$id}lorem_lorem={$url}\" ", $content);        }     }   }   return $content;}

Example script