Water purifier destroys water

Are you sure it's the purifier losing the water, and not your pump system?
Pumps and pipes will lose contents.

Good question, and I did check that.  When I remove the purifier from the same test, it pumps 94-97% of the contaminated water to the output reservoir.

I also just got done doing another test.  I've heard about a "falling water" bug, so to take that out of the equation, I did this setup:

Contaminated water => pump => purifier => 100 stretches of pipe => valve (turned down to 10g/s) => output reservoir.  Started with 1000kg of water in the input reservoir.

Once the pump stopped being able to pick up new water and the remaining water was pushed up against the valve, 55 of the post-purifier pipe stretches held 10kg of water (550kg total), about 1.9kg were in the post-valve output pipe and reservoir (and for completeness, about 34g were left in the input reservoir.  So this was better than my first result, but still only 55% of the water made it through purification.

That doesn't eliminate a pipe-specific issue, I suppose - but does take vent / falling water issues out of the picture.  When I re-opened the valve and let it all flow out, the result was 550kg of output fluid.   So if there were any pipe issues, it doesn't seem there were any in the post-purifier flow at all.