Alexa camera original QTs are a bit “off” for lack of a better word. Not too surprising given the lack of any coherent documentation to guide developers on QT best practices. The QT API is a patch work that spans decades, and there are dozens of way to do things. The few Apple QT recommendations don’t work in FCP. ARRI simply picked a path that cause issues FCP.
I don’t know how much footage you have, but doing a “Save as…” in QT player should “fix” the ARRI camera original files. You can also try a batch Export in FCP or use CatDV to export new movies. You may be able to export reference movies which would save export time, but self contained may be necessary.
Once you have the new movies, re link them to your project and try your Media Manage again. I’d suggest doing a test using the above techniques to find which works the best and fastest before exporting all your Alexa footage.
Arri needs to fix their files.
John Heagy