Creating unique Numberlink/Flow Free is very difficult. If you look at my algorithm proposal in the mentioned thread, you'll find an algorithm that lets you create puzzles with the necessary condition that solutions must not have a 2x2 square of the same color. The discussion at http://forum.ukpuzzles.org/viewtopic.php?f=3&t=41, however, shows that this is insufficient, since there are also many non-trivial non-unique puzzles.
From my looking into this problem, it seems the only way to solve this problem is to have a separate algorithm for testing uniqueness, and discarding bad instances. One solver that's made precisely for uniqueness testing algorithm is Imo's solver.
Another option is to use multiple different solvers and check that they come up with the same solution.