I unplugged my headphones earlier today to use my monitor speakers for the first time, and when I plugged my headphones back in I had to apply a setting in Realtek HD Audio Manager. The default setting was 24 Bit 48000 Hz but there were quite a few options, with one going all the way to 24 Bit 192000 Hz.
I'm not sure how these work and I've heard that changing these could possibly ruin my headphones so I don't want to mess with them without knowing what it's going to do first.
But to answer your question directly, changing this setting will have absolutely no negative effects on your headphones. If you turn it all the way down to say 16 bit 44.1 khz, this will not effect anything really. If you have a really good stereo hooked up to your computer, you might notice a subtle difference, but not much.