Mmm. In the counter-example given on wikipedia, the two functions are still piecewise linearly dependent, meaning they are linearly dependent except at discrete points.
Normally, when you patch together solutions in different regions (where potentials are defined piecewise), you have matching conditions which ensure that the wavefunction is continuous, and that the discontinuity in [tex]\psi'(x)[/tex] is given by integrating the Schrödinger equation across that point. Thus, in 1D, you specify the WF and it's derivative at 1 point (remember, the SE is a second order equation), and the matching conditions uniquely give you the wavefunction everywhere else.
Therefore, you won't find yourself in a situation where there is an ambiguity in terms of how to patch up the solutions. It is unique.