Perhaps you did this already, but: tear the entire enclosure apart to make sure the snake is really not in there. I've had larger snakes than that hide really well in some pretty simple enclosures and freak me out.
Bogertophis hit all the main points about searching, but I'll add that the only hatchling milk snake I ever had escape (a Costa Rican Black, the largest milk species) left the house -- climbed out of the basement where he was housed -- and was found in the attached garage (got himself into an empty bucket and couldn't get out). So once you've covered the room, expand the search to adjoining rooms.
Maybe this is not for the faint of heart, but: rodent glue traps will catch snakes, and the snakes can be removed safely from those traps by rubbing the entrapped snake all over with vegetable oil. Just check the trap at least twice a day.
Going forward, remove the probe from the enclosure and use an IR temp gun to check surface temps of cool side, hot side and under the warm hide. (I assume you have a thermostat probe on the outside of the enclosure on the heat pad/tape -- continue using that one, of course). Unless you live in a literal desert, ignoring enclosure humidity is fine so long as you provide a moist hide (box with a hole in it, and half full of damp sphagnum moss); a milk is fine with ambient humidity and should have a moist hide to regulate its own desired environmental moisture levels anyway.
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