PP does not support AVCHD files which may cause choppy or missing audio/some video problems. Adobe says the solution to this is to burn the AVCHD files to a disk first before importing. I did for this for the problem clip and it solved the missing video problem, but there was still a missing audio track, and yes, I checked everything. Converting AVCHD files with Any Video Converter has worked in the past when using a different camera.
I think the solution is to burn just the audio to a DVD, in the case of very large files.
https://www.adobe.com/cfusion/search/index.cfm?cat=support&term=premiere%20pro%20problem%20with%20avchd%20audio&loc=en_US&self=1&lr=en_US&site=premierepro_all&product=premierepro