Oh, Elphaba! We've been there MANY times... and once that nose is clear he makes up for lost time like you wouldn't believe. Also, at 39 months she isn't likely to forget such joy as nursing.
DS went through a horrible spell of illness from 18 months to 2 1/2 and he would go days without nursing once he realized he was too stuffy to make it happen. I panicked at first and he would be so upset initially (frustrated that he couldn't nurse), but then calm down once he started getting the hang of the colds and the stuffiness would be over in a matter of days. As soon as there was one clear path in that nose he was hanging on me until he'd made up for lost time, and lost supply for that matter. Also, when he started being able to blow his nose, it helped.
Best of luck and hang in there!