It would use the next available tuner and the one you are watching would be last.
Did you notice the recording lights? How many lights are showing?
Your cable card may not be up to date if its recording at most 4-5 channels instead of the full 6.
You can try testing the tuners. When it is not recording anything,
Press Record and then Select, it should start recording on whatever channel its on. Change to a different channel and repeat. See how many channels you can get until it complains at there are no more available tuners.
You can stop recording by pressing Record and select Stop Recording.
Series 2 (PLS, sold)
TiVo HD 1TB (157 HD Hrs, PLS, "652")
Roamio! Oh, wait, Its Juliet!
OTA! OTA! OTA!
The TiVo Apocalypse begins on Sat 2013 Feb 16 00:00 GMT!