It sounds like maybe you are mixing the concepts of interference in waves (eg. "negative phase") and damping. Energy can be stored in the wave and/or it can be dissipated by damping, which is a term typically used to describe lossy processes. Interference can make the wave energy move around, or at least appear to, but it won't go away. If you really mean where does the energy go eventually, then it will be dissipated, usually as heat, in the damping mechanism.
While you can make the wave(s) amplitude go to zero via destructive interference, there will be other places where you get even more energy from constructive interference. It isn't lost by interference, except in a local sense.
If you describe your experiment in more detail, you might get a better answer.