I just discovered this bug tonight. In my case, I am not seeing the red "missing footage" track. My tracks look fine. I performed my merge and then cut & pasted clips from the top-level bin—where merged clips are put by default—into a lower-level folder such as Project/interviews/guest/A Cam. I then dragged all of my merged clips to the "New Sequence" icon at the bottom of the Project Panel. This created a new sequence where only a few clips suffered their in silence. In an attempt to perhaps restore the audio, I saved the project and closed Premiere Pro. When I re-opened the project, ALL of these clips were missing audio. Again, no warning message or otherly-colored audio track. Just silence where there should be beautiful sound.
ASUS G75VX Laptop w/ Windows 7, 64-bit
Intel i7-3630 (no integrated graphics)
16GB RAM
NVIDIA GTX-670MX w/ 3GB VRAM