Do you know that the WAV file contains only one RIFF chunk? If so, you can just strip off the first twenty bytes of the file. If you don't know, then you'll have to parse the headers to find where the chunks begin and end, and strip each chunk's header out individually.

It should be pretty easy to determine if there's more than one chunk per file or not. Search for the four-character strings "fmt " and "data". If you see more than one, chances are that it's got more than one chunk, and you'll need a vaguely intelligent program to fix it. If there's not, then you should just be able to strip the first twent bytes off.

Under unix, you should be able to

strings file.wav | egrep '(fmt )|(data)'

What OS are you using? Could Perl be used?