Based on what i have been reading on the forum, probably. Someone's run into a problem before when they included two copies of the fingerprints in one envelope with $18 fee. One set of fingerprints didn't come out good so the entire package was rejected without them looking at the second card since the fee covers only one set of fingerprints!! To avoid running into the same issue, I sent two separate sets of fingerprints in two different envelopes each with it's $18 fee. So, they will be two applications from their perspective hopefully. Those just got delivered yesterday so I dont know if they have issued two ref numbers or not. How and where to look? My case may answer your question right away. However, if you mailed both the sets with just one $18 fee, i don't think you will get two ref numbers.