People who are using MTS files with Adobe Premiere Pro(especially CS6, CC7) often have the similar problems Premiere Pro missing audio track for MTS files.
There are 3 ways that might help you resolve your work- Premiere Pro, MTS files, metadata and no audio:
1. Install an earlier version of premiere pro like 4 - 5 depending what version fits what you do......(DO NOT UPDATE!!!)
2. Import the ENTIRE CARD, very important, all the files from your card to your PC/Mac, the metadata should be located somewhere in a folder within the card, it's not on the .mts file.
3. Convert MTS clips into another format for Adobe Premiere Pro and relink against the transcoded version. It will get the audio back into Premiere. Might be a bit time consuming but it works. And Brorsoft MTS/M2TS Converter for Mac is what we recommend as the best MTS to Premiere Pro Converter.