Check out Adobe AIR 1.5 * Updating AIR applications. It probably doesn't handle FTP-based sources (HTTP: yes), but it is supposed to address the general problem you're facing. Quote:
[...]
Using the update framework
Managing updates of applications can be complicated. The update framework for AdobeAIR applications provides APIs to assist developers in providing good update capabilities in AIRapplications. The functionality in the AIR update framework assists developers in the following:
- Periodically checking for updates based on an interval or at the request of the user
- Downloading AIR files (updates) from a web source
- Alerting the user on the first run of the newly installed version
- Confirming that the user wants to check for updates
- Displaying information on the new update version to the user
- Displaying download progress and error information to the user
[...]