I am having a similar problem today. A few days ago, my notarization was working perfectly and notarized within 30 - 90 seconds. But today, it is constantly stuck "In Progress". There was apparently server maintenance completed this morning - not sure if that had an impact.
dsimpson
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I found that it was tedious to make these changes manually, so I wrote the CFBundleIdentifer Fixer app to solve the problem.
The solution is straightforward, just use the CFBundleIdentifier for the main app as a prefix for the CFBundleIdentifier values within each enclosed bundle plist file.
===== Usage Instructions =====
1) Launch the CFBundleIdentifer Fixer.
2) Drag & Drop the app you want to fix onto the application button.
3) The embedded bundle plist files will be updated and the results displayed in the Results field.
4) After fixing the CFBundleIdentifiers within an app, your app will need to be digitally signed. You may use command line commands or automated tools like App Wrapper to perform this signing.
This app is available on the macOS App Store and on the FmProMigrator.com website.