I've converted a few albums encoded in WMA Lossless (through WMP) to FLAC through foobar2000. It is quick, easy and completely lossless. To verify, I tested to see if the resulting files that came from HDCD would be recognized by my AVR as having HDCD data. As expected, the resulting audio is still recognized as such.
By the way, there is now a DVD-Audio decoder available for foobar2000. I've converted DVD-Audio tracks directly to FLAC with no issues. There is a thread about it in the Surround Music Format section of AVS if you didn't already know.