We did this tonight! My DD2 is 15 months and with another on the way I'm avoiding the hassles when I'm bigger. We still have the cot in the room, right next the bed actually, acting as a 'wall' (we have a pool noodle under the bottom sheet to be a stopper for her falling out on the not against the wall). We'll take it away in the next day or so.
With DD1 she was about the same age and we just got her all excited about the bed and the cot didn't ever get built in her new bedroom (we shifted and decided with a new house, new room, we'd do new bed too). We didn't have a problem.
So, that's a long winded way of saying tell him he's in the bed, but if keeping the cot there for a couple of days gives you and him peace of mind, then do as PP said and take it down with him helping in a couple of days.
And if it makes you feel better - there's someone else doing the same right now too!
Isobel 19/7/06 Molly 14/2/08 Sam 4/10/09