Every year the Republicans alienate a little bit more of their base. For a while it was the Tea Party, and now it's the people who supported Ted Cruz. As they alienate their base, the Libertarian party grows a little bit at a time. This will continue into the next election cycle until their is nothing left for the Republicans.
Republicans will continue to desert the party. The strongest reason is the Republican party does not represent the views of the people of the Republican party. For years the elected officials have been more interested in maintaining their power and control. The elected officials do not carry out the wishes of the people who elected them. This means that the people will continue to look for candidates who will carry out their wishes.
Sure, some Republicans are deserting the party this year, but the same can be said for the Democrats. Their convention was completely split, and there are tons of Sanders supporters who will never support Clinton. In the end, I think most people will return to their parties because there is no viable 3rd alternative.
No, the desertion of many Republicans from the party will not necessarily last into the next election cycle. Those who are deserting are doing so because of one candidate. By next cycle, most people will have forgotten the problems of this election and will have moved on to another. The outcomes of that election will depend on the new candidates and the actions of those elected this time.