If you slip properly, you shouldn't be changing your level enough to have to worry about knees. If you become too predictable or time it wrong, you can however slip right into a headkick.
In kickboxing your best bet with slipping is to only slip one punch and to return fire immediately. Trying to move your head away from several is really just setting yourself up to eat shin. (This is something I learned personally when I returned to kickboxing after several months of just boxing.)
Because the range is longer in kickboxing, I'd suggest pairing your slips with footwork rather than just slipping in place. While there will be times that you can slip and counter without moving your feet, there are even more instances when you won't be able to reach him with your counter punches without advancing.
So here are the two safest ways to "slip 'n rip" in kickboxing (that I know of).
Slip the jab, return with the cross. Because a lot of Muay Thai practitioners don't step heavy on the jab, you might want to do this coming forward so you can actually reach with your punch. Step forward slightly with your left as you slip; it'll give you a few more inches of reach.
Slip the cross, return with the hook. Take a small, diagonal step forward with your left as you slip. (If you step straight in, you'll run right into his cross. Cutting a small angle with save you.) Rotate your hips all the way through on your counter hook. Don't be lazy with it!
Slipping the cross is great because after the hook you've got so many options -- assuming you rotated enough. You could throw a cross right after, you could cut across with a springing kick since your hips are wound up, or you could pivot on the hook and throw a body kick after.
As for actual slipping technique, rotate your shoulders and hips when you're slipping a jab. Make sure your weight shifts on to your rear leg so you're primed to return with a cross. Rotate your shoulders, hips, AND rear foot when you're slipping a cross. Your weight should shift on to your lead leg, so you're primed to return with a hook.
Point the shoulder when you slip and bring your hand to your cheek. Don't try to slip like Tyson (side to side, no shoulder rotation) and don't drop your hand as you do so, in case a kick is coming.
ABSOLUTELY BRILLIANT ANSWER THANKS MATE!! I REALLY APPRECIATE YOUR TIME AND EXPERTISE!!!
THIS HELPS A TONNE!!