Strings replace in bash using multiple lines pattern

You could convert all of the relevant text strings to hexadecimal strings, perform the replacement in hexadecimal, and then convert the result back to text. Here is what that might look like:

#!/bin/bash
# replace.sh

# Set the target string, i.e. the string to replace
read -r -d '' TARGET_STR <<'HEREDOC' 
    $N = "magic_quotes_gpc = <b>"._("On")."</b>";
    $D = _("Increase your server security by setting magic_quotes_gpc to 'on'. PHP will escape all quotes in strings in this case."); 
    $S = _("Search for 'magic_quotes_gpc' in your php.ini and set it to 'On'."); 
    $R = ini_get('magic_quotes_gpc'); 
    $M = TRUE;
    $this->config_checks[] = array("NAME" => $N , "DESC" => $D , "RESULT" => $R , "SOLUTION" => $S , "MUST" => $M );
HEREDOC

# Set the replacement string, i.e. the string to replace the target string with
read -r -d '' REPLACE_STR <<'HEREDOC'
    /* NOTE: "Magic_quotes_gpc" is no longer required. We taught GOsa2 to deal with it (see /usr/share/gosa/html/main.php). By Questor */
    /* Automatic quoting must be turned on */
    /* $D = _("Increase your server security by setting magic_quotes_gpc to 'on'. PHP will escape all quotes in strings in this case."); 
    $S = _("Search for 'magic_quotes_gpc' in your php.ini and set it to 'On'."); 
    $R = ini_get('magic_quotes_gpc'); 
    $M = TRUE;
    $this->config_checks[] = array("NAME" => $N , "DESC" => $D , "RESULT" => $R , "SOLUTION" => $S , "MUST" => $M ); */'
HEREDOC

# Set the path to the input file
PATH_TO_FILE="target-string.txt"

# Set file paths
PATH_TO_HEX_FILE="${PATH_TO_FILE}.hex"
PATH_TO_REPLACED_FILE="replaced-${PATH_TO_FILE}"

# Convert the two strings to hexadecimal
TARGET_STR_HEX="$(echo "${TARGET_STR}" | xxd -p | tr -d '\n')"
REPLACE_STR_HEX="$(echo "${REPLACE_STR}" | xxd -p | tr -d '\n')"

# Conver the input file to hexadecimal
xxd -p "${PATH_TO_FILE}" | tr -d '\n' > "${PATH_TO_HEX_FILE}"

# Perform the replacement using hexadecimal strings
sed -i'' "s/${TARGET_STR_HEX}/${REPLACE_STR_HEX}/g" "${PATH_TO_HEX_FILE}"

# Convert the result back to text
xxd -r -p "${PATH_TO_HEX_FILE}" "${PATH_TO_REPLACED_FILE}"

# Remove intermediate file
rm "${PATH_TO_HEX_FILE}"

This produces the desired result for the test data your provided.