Will this affect gameplay at all?
Mathematically speaking, you could get to every possible board setup using only one key card. The problem there is that players might learn what that setup looks like. You could still probably get by with only 5 or 6 key cards as long as players didn't intentionally try to memorize them. Having only 39 instead of 40 will make almost no difference.
(That said, if it bothers you or your friends to have the odds for which team starts be slightly off of 50/50, you could use the app in place of key cards.)
CGE are very friendly and would probably be happy to replace the missing card, but figuring out which one needs replacing might be more trouble than it's worth.