Both inputs (mic & lin-in) will mute if the input level is set to "0". So be careful if you are adjusting input levels on the recorder and are near the bottom of the input range or you may inadvertantly mute the input if you go to low.
The jury is still out on how the gain structure works in this thing. We won't know the best way to run it until someone does some bench testing or noise listening tests. Using mic-in obviously adds gain as the record level is increased. If you are using an external preamp, you'll most likely go line in. How the level control for the line-in works is still in question. It may add analog gain as the control is increased, may add digital gain, or may just attenuate the signal.
That is a very good question, and got me going on a science project to answer it, since I plan on using my R-09 often. I sent out a line level 1khz tone from my stereo, mini plug out. Then recorded this on my JB3 which has a setting for 0 gain. This produced a constant -17db signal checked in wavelab. Then I switched to my R-09 and recorded different line-in gain settings to get the same -17db checked in wavelab. This turned out to be 8.
So here is my theory of how the R-09 line-in works, if you set it below 8 you are attenuating the signal, all the way down to 0 which is 100% attenuated, no sound. And any setting above 8 is adding gain. So if you have a super nice preamp that you want to use, set the R-09 to 8 and then use the controls on the pre to set the levels after that.
The pre on the R-09 sounds decent, so it would be great to hear a comparison of a commonly used high end pre recorded with the R-09 line-in set to 8, versus using only the R-09 pre and mic in with gain adjusted to match the saime record levels.
