I think it's not difficult to build a new installer with exactly the previous content, signed with a new certificate.
Since an air installer file is just a zip archive, you can unzip it and rebuild with the same version of the SDK that you have used for the original installer. Preferably you should have access to the original *app.xml that you had used for the original build, but you can also create a new *app.xml from the application.xml file in the archive.
All that's left to do then is run the correct version of adt, telling it to create an installer from the content you have just unzipped, using your new certificate to sign the code. I did this, it's not a big task and new customers are installing from the new air file.
As an aside I'll add that I've given up on air installers; I find their main merit to be the job security they provide for support personnel. The new version of our software is distributed as msi and dmg files.