Not precisely as you have defined it, if it is mixed with other sounds, and here's the reason; consider the effect of a wave mixed precisely with its inverse; the result is flat response. The mixing of waves can have a monotonic function, that is, to effectively mask one wave with another in a way that the first is unretrievable.
That said, there is likely a way of characterizing the "signature" of a wave such that it is likely to be present in a resultant composite wave file, but that signature would depend on the length of the wave file and to some extent what type of combinations were expected to be done upon it.
Your question probably has something to do with determining if samples of one work exist within another, composite, work. In general, yes, FFTs are useful for determining a "signature" for a given wave, and being able to extract that "signature" from another wave; they're good for some things (such as frequency shift; it just shows up as a displacement on the FFT), but not so great for other things (varying frequency modulation, for one; high (or uneven) bandwidth compression of the original signal). To put it another way: FFTs are a good way to detect "naive" use of samples, but a determined resampler can modify the original sample to make it hard to detect via FFT if he knows that that is the detection technique used.