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Question about left/right or splitting lines

i am just about to embark down a path of spliting up my signal into two paths(either left/right or just two seperate) to allow different pedals to effect that line and then combine back at the end of the pedal board.

my question is that if one side is switched off, will the signal try to flow backwards down the other line as well as out to the amp. and will this hurt the non-used pedals?

hope that made sense.
 
Without a proper buffering / mixing system, what you describe could happen, but it will cause feedback and/or tone suck instead of damage to your pedals. One other problem that may occur is phase canceling; this happens when a pedal inverts your signal (some do), then when you blend an un-inverted signal with it you get two opposite electrical signals canceling each other out.

A Link Removed is a real solid solution to your problem, or you can get something like this which has a slightly different set of abilities.

Both of these buffer your signal, split it into two signals, and then blend the signals back together at your desired position. The Boss has some boost built in which the other doesn't, but the ebay one has a little more functionality with using one loop at a time and a phase inversion switch.
 
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You can, and I did for a while, but it can be a PITA if you want to start using one loop or the other independently of each other. You'll want to make sure that it's not a passive unit otherwise you'll have the same problems with combining them at a cable. You will still want to have some kind of a buffer before the split to keep your signal from getting loaded down. Buffer can be a buffered pedal, active bass, or any always on pedal.

Good luck and have fun.