As MerryLore said, the duel is still on, and completes later when an opponent is found to battle you.

I think it might be useful for me to suggest a model for what's going on, which will serve to organize discussion of what happens in a duel. In this case, I'm talking about duels between houses, rather than specific users; I think most people are fairly clear about what happens in duels between specific users. One person starts the duel, and when the other person responds, the duel completes.

In the case of duels between houses, however, the matter is more complex. Suppose you are in Ravenclaw house, and you decide to duel a Gryffindor. We might call you, therefore, a R->G duellist.

When you start the duel, you cast the spell, and you earn a score. To complete the duel, however, your score must be compared against that of a corresponding G->R duellist (that is, a student in Gryffindor house wishing to duel a Ravenclaw). There are a few possibilities. One possibility is that by the time you cast your spell, there are already G->R duellists who have cast their spells and are just waiting for their scores to be matched up against someone else's. In that case, one of them is selected to match with you, and your scores are compared to determine the outcome of the duel.

Otherwise, however, you will have to wait for a G->R duellist to show up. It may even be that there are a few R->G duellists (like you) ahead of you in line, in which case you will have to wait for an equal number of G->R duellists to show up before one will be matched with you. At that point, whenever it happens, your scores are compared to determine the outcome of the duel.

I'm in Ravenclaw, and out of a tactical awareness I prefer to duel Gryffindors and Hufflepuffs. I've found that I generally have to wait quite a few hours for G->R and H->R duellists to show up. I suspect that's because other Ravenclaws (with the same tactical awareness) are predominantly duelling Gryffindors and Hufflepuffs, and are outpacing the Gryffindor and Hufflepuff duellists. I think this supports the above notion of how the duelling server works.

Incidentally, this matching task, which the Pottermore servers much execute, is often called the rendezvous problem, because it requires that the servers bring together two users with complementary properties. (In this case, each student wishes to duel someone in the other student's house.) We also see it in on-line dating, job resume sites, and the like. At the very beginning, Pottermore tried to schedule all duels between individual users. However, because they only displayed the first three or so users waiting for partners to duel, everyone tried to duel the same three users. As the number of users increased, that system clearly became unworkable. They recognized that most users did not care about which other individual they duelled, provided that the partner was from the right house. So they changed their design to the current system, which is far better able to adapt to large numbers of users. It's a good change, but they probably had to first come up with the idea, then re-engineer the duelling processes, so it did take a while. Some of us also speculated that they were working on multiple projects at the same time.

At any rate, this is probably much more than you needed/wanted to know, but I think it is worth having a specific model of operation in mind, so that some of these explanations make a bit more sense.