Are people still spouting this nonsense about FLAC sounding different or "lowering the quality"? If it sounds different then there's something wrong with the player you're using or you've corrupted the file.
If you don't believe that the FLAC file is identical to the original, open up both the original and the FLAC version in an editor (such as Audacity) and compare them. You'll find they are BIT IDENTICAL.
That magazine is clearly either written for by idiots, or trying to create drama from nothing to sell more copies, maybe a bit of both.
Regarding and reconstructs it perfectly afterwards. It's not a "lower quality version" when compressed, it's not audio data AT ALL when it's compressed, it's purely encoded data and no-longer RAW WAVE (just as a RAR file won't be a lower quality version of your Word Document or Spreadsheet when compressed).
For anyone else that feels the need to say something silly, please see - http://en.wikipedia.org/wiki/Lossless_data_compression - first.
Oh, and to answer OP's question: Foobar2000.