Modifying the conversaton using CDE Studio (or any other means) is not supported by TAC or the BU - this is why the CDE STudio requires a key to open it up. You'll also notice the script files are "water marked" with CRC codes - folks that try and hack up the files on their own cause the CRCs to not match and errors are logged to the event log each time that conversation is loaded. TAC will ask you to reload the production scripts if that happens.
Obviously for support reasons it's difficult at best for us to support sites hacking up their conversations in the field. Is there some specific conversation flow you're trying to change that you can talk about? There may be other options here.