I wrote a batch file that runs the conversion and writes the stderr to a text file, it then parses the text file to see if it found HDCD (if it didn't it just crashes or writes an identical file). If it did find it it copies it back to the input location and moves on to the compression if not then it deletes the file. One issue right now is that I put it in the WMA compressor VBScript file to call the batch file.
In the end it works rather well.