It bypasses the volume control on the pre when you are listening to 5.1-7.1.
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It works as a unity gain for your preamp so that volume when watching movies/TV is set by your pre/pro and not the preamp. This avoids the situation where the last time you were rocking out to your 2 ch system and shut the system down with the volume way up and the next time you go to turn on your HT, and the combination of the two volumes blows out your speakers. The bypass kills the volume on the preamp so that volume is controlled only by the pre/pro. Essential feature when incorporating HT and 2 ch. You can find unity gain on the preamp and set it there before turning on the pre/pro, but that one time you forget......
The home theater bypass feature allows you to use your two stereo speakers as your Front Left and Front Right speakers in a home theater setup as well. Basically you take the FR & FL line outputs of your HT receiver or SSP and run them into the HT bypass of your stereo preamp. Most HT bypass' are unity gain, which means that the volume control on your HT receiver or SSP will control the level of all of the speakers.
I hope this helps.
Some do not realize it is fairly easy to connect and integrate your your home theatre with your two channel system, even without the HT bypass. The benefits of the HT bypass are essentially the convenience of pressing just one button to switch over control of your 2-channel system to front speakers in an HT or 5.1/7.1 system, and the potential sonic benefit of having the preamp volume control out of the signal path when playing your HT system. If you do not have HT bypass on your preamp, simply connect your HT front channel line outs to one of your preamp inputs, then select the volume level that corresponds with unity gain (JA often reports this when reviewing preamps for Stereophile - often around 11-12 o'clock on the volume knob). If you do not exactly know where unity gain is on your preamp, simply use the gain adjustment on your HT processsor to set the appropriate front channel gain for a particular preamp volume control setting, then use that same volume control setting on your preamp each time you play your HT system. Just remember to turn the volume down when you are done watching movies, as Stew3859 pointed out.
As mentioned it allows a decent 2 channel preamp to be used in a home theatre set up as well, allowing for a hybrid two channel/ht system.
BUT, some HT bypass preamps are better designed than others. While some are unity gain units (as mentioned) they still process the signal and can impart a sonic signature which means that the 2 towers in a ht setup will have a slightly different sonic signature from the rest.
Other manufacturers, such as Cary, have a true bypass circuit. The entire preamp is bypassed so that no processing of the signal occurs. In fact, the unit can be turned off in bypass mode to save tube life in the Cary tube preamps.
I have considered the high end HT processor option but HT technology evolves so quickly that within a year or two, it will be obsolete (HT-wise) and need replacing, whereas a stereo preamp with true HT bypass can be kept in place until the upgrade bug hits (hopefully a long, long time later). To me, therefore, a better (mostly because it is more cost effective in the long run) solution is a pre-amplifier with true HT bypass.