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Not sure about the audio issue, I'd try reimporting the audio and see if that fixes it.
SWF content not publishing with HTML5 is expected. They are two technologies that aren't compatible.
Here are the known behaviors for publishing with HTML5:
Can I convert the files to something else?
Any ideas on what is compatible?
I did try reimporting the audio with no luck. Maybe its related to the SWF files on the same page.
If the audio issues are on the same slides, then I would say it is safe to say they are related.
Converting the SWF's depends on what level of interactivity you are looking for. If they are non-interactive, you could just convert them to FLV or MP4 videos and they should work. If they need to be interactive, then I'm not sure what your options would be. There may be some other users who have made this conversion, but I'd have to dig to see if I can find an answer.
They are interactive. I am trying to build a training for an iPad. Clearly there are interactive graphics for iPads out there... I just can't figure out what file type they are.
Thanks for the help!
They are likely HTML.
You may want to look into Captivate and it's ability to publish as HTML5. It is more capable, but SWF content will likely have the same issue no matter what tool is used. Ultimately SWF content is Flash content and that is no longer supported on mobile devices.