Did it Jamie.
around the same question, the fact that the container ID is not unique on a project scope due to code reuse such as template and copy & paste.
dtsutil.exe is great on a package level because it renumber the package, but does not the trick for containers unfortunately. And I've seen no ways of changing it manually.
What would be the trick? find and replace with a text editor on the xml file ?
Regards,
Franck