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Better way for me is to put a sensor, then the shutoff on a straight pipe. That is you put a straight pipe, let's say 4 tiles long, you put the sensor on the first or second pipe tile, then the shutoff to head water or other out of the main way, and if you don't have any bend just after the shutoff, it should work fine (at least it works for me).
You have also to be sure there is no back up at the output of the shutoff, or water that should go through the shutoff will simply go the other way and ruin your intentions...
EDIT:
Here are screenshots. A bit complicacted a first view, but this is how I sort liquids with a first sensor for germs, sending the liquid to chlorine room, and sending it back to the loop.
All sensors and shutoffs are on the same loop, one after the other. This fixes the back up issue on one of the shutoffs. In case the output of the shutoff is full, liquid goes forward in the loop. Actually it moves the backup at the entrance of the loop, if the loop gets full of liquid running round...but this is much less impacting and easier to manage.
I know it's not very evident as this configuration has been modified in the run according to my needs. It has to be reorganized, but it works perfectly.
I send into the loop (always through a bridge not to block the loop itself) all the liquids I need to sort into dedicated reservoirs, and I never had any mix so far. Contaminated liquid goes to decontamination and comes back to the loop to be sorted...
https://steamcommunity.com/sharedfiles/filedetails/?id=1908403536
https://steamcommunity.com/sharedfiles/filedetails/?id=1908403624
Hope it helps... Sorry my English is a bit poor sometimes.
Btw, idk why but in sandbox mode when my pipe started to pump water with germs, the water in pipes was without germs or with like nearly noone, even thought water in "place" had like 400k+ germs on start.
But maybe you did it and there is some other reason I don't see just now.
Have a good game