Here is a little script we wrote to help re build Enterprise iPad apps without having to checkout the project and re compile them.
Saves a lot of time when simply adding a new provisioning profile as you don't need to checkout the source or re-compile the project. You can do the whole thing from an existing ipa.
You just need the ipa, the new provisioning profile and an enterprise certificate.
It also allows you to update the version, the bundle id and some other options.
It does use Apple Dev tools, so you will probably need the Xcode dev tools installed.
A simple example:
/resingipa -i test.ipa -p com_domain_app.mobileprovision -c "iPhone Distribution: ACME Ltd"
More examples in the git hub repo.