CNC cut depth > flute length?

I’m trying to wood CNC a 2" deep pocket (in hardwood). I have a bit that has a 2" flute length but it is 1/2" in diameter. I would prefer to have a smaller radius on the pocket. I can find a 1/4" spiral bit with enough length to get to the bottom, but the flute length is only ~1 in. I assume this would not work, since the shaft would be rubbing against the pocket wall?

So you have a 1/4” bit with a 1” cutting length and over 1.5” of shaft, so that you could leave more than an extra inch of shaft exposed and still hold the bit securely? You could probably do it if so (though that is an odd bit). You’re right that the shaft would rub a lot. You should certainly do the cut with the 1/2” bit first then come back to clean up the corners. Given how much that small bit could flex over that length, I would lower your feed rate or cut width or both.