Just a thought, and it might not apply, but in the Timeline, PrPro relies on the CFA (Conformed Audio), and the PEK (Waveform Display) files.
When on Imports source files with Audio, PrPro needs to Conform and usually Index the files. If that process does not complete, then behavior, similar to what you describe, can occur. This ARTICLE goes into more detail.
Did anyone ever isolate a solution for this. I am running into the same problem and no-one has answered me, Adobe won't even call back.
Happened to me today. Deleting the Media Cache files and Cleaning the Database solved it.
A bit same pb happen to me. The cut was OK I close it and a few days after open the project and the sound was in RED. Also all the rush were offline.
My rush were in : AVCHD 1080p - Pixels carrés
Base de temps : 25,00 i/s
My solution is to copy in the same directory the rush (for exemple 00002.MTS become 00002_2.MTS) and to reconnect in Premiere the rush 00002.MTS with 00002_2.MTS. (don't know if I am clear !).
This solves the problem for me.
Rq : if I clear the original file (00002.MTS) an rename the 00002_2.MTS in 00002.MTS the error is back ! Stange !
I have encountered the same issue and it is a huge pain.
Just now I realized that you can select all of your audio, right click and select "Audio Channels." You will notice that "None" is currently selected. Change the setting to which ever channel has the audio (if you are using two channels select one for right one for left--not tested, will probably work). And voila, reconnected.