Very aggravating, and through experimentation it seems to propagate.
Expected results:
Pipe Germ sensors will detect 0 germs in an empty pipe and 0 germs in a pipe with liquid that has 0 germs. If liquid in a pipe has germs the sensor can detect, this would be visible via inspecting the water in the pipe.
Actual results:
You will see the Pipe Germ Sensor detects small amount of germs (usually less than 30) even after germy water has left the pipe. Compare this to water in your pipe: it will detect germs even when the water in the pipe is clean or even when the pipe is empty.
It might be magical thinking, but it feels like what happens is if 10kg of germy liquid goes through the pipe, the germs linger even after the liquid has moved on. It's possible to get out of this be letting a lot of liquid flow through. This means setting up a flushing system, or increasing the germ sensor tolerance to just above the germ count, eventually it usually drops back to 0. This is not a desirable work around. You can also see the germ count sometimes go up as new clean water enters the pipe -- or even when it sits there empty (despite being in chlorine).
Save game as picture with 20 magic germs: First Out.sav
Step 1: Build a 3+ reservoir cycle in chlorine hooked up to toilets and sinks in a closed loop, with filtration so that you never store polluted water. OR use my save game and skip to step 4. My save game has 20 germs detected in an empty pipe.
Step 2: Set up locks and timers so that no tank can flow directly into another, and so that water will last long enough to kill germs (half a cycle is usually more than enough, have your first tank finish emptying right before the first wave of dupes use the toilets)
Warning: This will put a minimum of 10kg of germy water into pipes where they are somehow immune to the chlorine. Pre-seed your tanks with 10kg+ of water each to help avoid this... or even easier, disable the tanks to start so that no water escapes and all germs are removed before you let the liquid through the first time.
Step 3: Setup a pipe-germ sensor right after your last tank, before the timer lock. Have this open a valve to redirect germy water to your first tank if any germs are detected.
Step 4: Let this system work it's magic. It will be fine 95% of the time. When it backs up and/or breaks down because water is stuck in a loop, look at your germ sensor.
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