As of 8/7/14, Twitch made the announcement that they have partnered with Audible Magic, a company that works closely with the recorded music industry, to avoid potential claims of copyright infringement for the use of in-game audio. Mind you, these changes are stated to only impact VODs (Videos On Demand), better known as archived broadcasts, and NOT live streams. This change is retroactive, meaning that it will impact both previous and more recent archived streams for all users. Twitch does provide its users with the option of archiving their broadcasts, with the majority of users being able to access their previous broadcasts up to 14 days later or beyond.
According to the announcement, Audible Magic scans all VODs in 30-minute increments, and in the event that it finds copyrighted music within a single 30-minute block, it will MUTE the ENTIRE 30-minute block! Again, this will only impact the VOD or archived broadcast. The muted portion of a VOD will appear as a red bar in the progress bar at the bottom of the video along with a notification that 3rd party content was identified.