You can search your pub id with in all your pages from your code editor, that means you will find the pages with your adsense code. Those pages not appeared in the search result that means they don't have your adsense code or other pub id is there. Then you need to open some "not appeared pages" in the search result and try to find the adsense code in those pages and then check the pud id. If adsense code is there that means this is adsense code with other pub id. Then you need the replace other adsense code with your own or you can use php include.
You're my hero. To the OP: How is it encoded? Unless it's JS just spider it with something like XENU and output all of the files, and search them for your adsense ID.