Ratification of the proposed constitution was on thin ice anyway. The 3/5 compromise was a Hail Mary pass. Failure would have left what was left of the post Revolutionary Confederacy with two giant states (New York and Virginia) and a bunch of smaller ones. Remember Virginia at the time stretched to the Mississippi River, theoretically, and included what is now Tennessee, Kentucky, Ohio and Michigan.
Not to mention a strong presence in the region from Spain and France...