Believe it or not, as the case for many seemingly-simple problem, the answer to this can be rather lengthy. For example, if you are talking about two oppositely-moving overlapping waves, then the energy conservation comes in because the location of destructive interference is still moving (i.e. it may have an instantaneous zero amplitude, but it still has a kinetic energy).
A very thorough discussion of this can be found in a paper written by N. Gauthier "What happens to energy and momentum when two oppositely-moving wave pulses overlap", Am. J. Phys. v.71, p.787 (2003).
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