a.js

// many many codes
document.write('foo bar');
document.write('</div>');
// new code
var a = 'bar.js', stamp = +new Date() + '=';
document.write('<script id="foo" src="' + a + '?' + stamp + '"></script>');
// other code
document.write('<div> other text</div>');

b.js

// many many codes
document.write('foo bar');
document.write('</div>');
// new code
var a = 'foo.js';
document.write('<script id="foo" src="' + a + '"></script>');
// other code
document.write('<div> other text</div>');

output.md

> ./replace.sh > new-b.js
> diff -u b.js new-b.js
--- b.js	2013-04-22 17:52:11.756024531 +0800
+++ new-b.js	2013-04-22 17:58:32.828017570 +0800
@@ -2,7 +2,7 @@
 document.write('foo bar');
 document.write('</div>');
 // new code
-var a = 'foo.js';
-document.write('<script id="foo" src="' + a + '"></script>');
+var a = 'bar.js', stamp = +new Date() + '=';
+document.write('<script id="foo" src="' + a + '?' + stamp + '"></script>');
 // other code
 document.write('<div> other text</div>');

replace.sh

#!/usr/bin/env sh

sed -n '
  /^document.write(\'<\/div>\')/ {
    n
    :start
    /id="foo"/! {
      N
      b start
    }
    p
  }
' a.js | sed '
  /^document.write(\'<\/div>\')/ {
    n
    :start
    /id="foo"/! {
      N
      b start
    }
    r /dev/stdin
    d
  }
' b.js