How to migrate your AIR certificate (Air 2.0)

1] Determine your application's current publisher ID. In an installed application, this is found in the package's META-INF/AIR/publisherid file.

2] Open your application's descriptor file, e.g. My-App.xml and add in:
<publisherID>mypublisheridstringfoundinabovefile</publisherID>

3] Export a release build with your new certificate

4] Run this command to tell adt you are migrating from a old certificate:
#/Applications/Adobe\ Flash\ Builder\ 4/sdks/4.1.0/bin/adt -migrate -storetype pkcs12 -keystore ./src/MYOLDCERT.p12 -storepass MYCERTPASS -keypass MYCERTPASS my-app-v2.air my-app-v2-migrated.air

Point your application's updater to my-app-v2-migrated.air and it should update fine