Nope, it's just letting you know that it killed part of your header. The wave data itself is still the same. Your decompressed wave will be the same as the original, however, the header data will be slightly different.
I don't know of a program off hand that lets you look at a wave header, but if you could do that, you can see what the exact header differences are between your master and the decompressed FLAC.
Again, I must stress that none of this affects the wave data itself.