I've used a TM900 for about 2 years and on a few occasions (less than a handful), in my video editor I've come across scenes with no audio. Nothing special about the scenes and they had the same settings as adjacent scenes which had their audio.
The first was a concert situation (which was a bit embarrassing) another just a street scene.

Has anyone encountered this problem?.

Hi Erik,

Since no one has responded yet I'll just chip in and say I have not had this issue with my TM900 (so far, fingers crossed). It does seem odd - and no doubt it is very frustrating for you that this is happening.

I know it's always difficult to track down faults like this. I'm wondering if it's a software thing (NLE on your computer or maybe in the camera) or a physical loss of connection (loose soldered joint within the cam's audio circuit somewhere perhaps).

Was this with a plugged in mic or using the in-built TM900 mics?

I was using the internal camera mics and the problem was definitely on the camera (not the NLE).

Actually, it has only happened twice - in probably about 100 hours of shooting. But the 2nd occurrence was recently and I am hoping it doesn't start to happen more often.

Like you, I was thinking it might be an intermittent joint, but if so it's very intermittent.
It is very definite, ie, there is absolutely no sound. If it was a bad joint, you'd think you'd hear distorted sound a bit.
It might be a software glitch. Weird things can happen with unusual combinations of options. Problem is the shots were just normal shots , same all the others.