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I have created an app and tested it on my iPad using Flash Pro CS5. When I try to export my second app I used the same .p12 Certificate and Provisioning Profile but when I load it into iTunes it overwrites my existing app. Do I need to use a differant Certificate or Provisioning Profile for every app that I export to stop iTunes from overwriting?
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You don't need to use iTunes to place apps onto your iPad. You can expand the IPA file (it's just a zip file) and drag the .app file in the Payload folder onto your device in the Organizer window of Xcode. That alone will save you many hours!
Back to your issue though. When you make an App ID in the Apple portal, you want to make an exact ID for the version that you upload to the App Store. So, perhaps com.mycompany.myappname. But for testing you can make an App ID that is either com.mycompany.*, or even just *. In Flash, where you have to enter the app ID, you put in something that matches that App ID. For your first app you would say com.mycompany.HelloWorld or just HelloWorld (depending on whether your App ID is com.mycompany.* or just *), then for your next app you would use com.mycompany.GreatApp or just GreatApp (again, based on the format of the App ID).
For all my testing I use the same Apple App ID of * and then use just a one word ID in Flash. Then the different apps won't overwrite each other.
Once you are ready to upload the app to the Store, change both the provisioning file to a Distribution one, that was based off of a full size App ID (like, com.mycompany.ReadyToUploadAppName), and use the Distribution certificate, and publish the app from Flash for App Store.
For the uploading part, unzip the final IPA, copy the .app file in the Payload folder to somewhere else, and zip compress that .app to be your submission file.
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So I only need different App IDs?
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The <application><id> entry in the descriptor would be different for each app, but they can all still use the same provisioning file, so long as the format of the App ID that the provisioning file was based on is compatible with the ID you use in the descriptor file.
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By the way, did you solve your uploading to the app store question? By chance I answered that in my other reply, but I notice that you were unfortunately a victim of them shutting down the iPhone packager area before anyone had a chance to answer your question!