First question is still... What's the point of this re-routing?
I personally send the audio signal from my SB X-Fi (through SPDIF) to my decoder (Z-5500) and it works great,
Sending the audio signal through HDMI to your TV creates more headaches because you have to use either ATI's built in Audio chip for this either nVidia's way of routing the audio signal,
If it's only for DD/DTS/AAC (up to 7.1) audio tracks I'd stick to sending the audio signal directly to your decoder,
And to answer your question, I (personally) think that will not alter the signal whatsoever if you re-route it through your TV,
e.g. what could change the audio quality will be using the DSP of a dedicated audio card for the decoding instead of your decoder itself
hope that helps you a bit
PS; re-routing the audio through your TV could be a good idea for HD audio contents (like DTSHDMA or DTRUEHD) because the SPDIF doesn't simply have enough bandwidth and you'd have to use cinch cabling