If you have a set left that doesn't depend on the result of the problem still in computation you can do this, yes. Though in that case you don't actually have two sets, you have one set which is bigger than your core count. I simplified a bit before, but if you have more problems than cores your longest sub-problem shouldn't run longer than the time it takes you to compute all other sub-problems (i.e. that includes computing five sub-problems on one core while another core computes one longer problem) or you'll have to wait.

Unfortunately, I had this happen to a program of mine last year. All other tasks were long done but one kept running and running. The run time of the program escalated to hours with the first few minutes being marked by high usage of the system and then only one core in use, while everything else had to wait. It sucked.