Why does fluid stop in the middle of a stretch of pipe?

I thought slushing was a problem and this would reduce it, if anything.
Why does this reduce the throughput down to 0?
Would it be better to just have nonuple pipe connected straight to the tank with a filter cover or nonuple pipe->filter+drum->pump->(pipe->)tank? The latter is what I have in a few places on my distilled water return pipe, hoping that it reduces slushing.

EDIT:
What is the best option when you need to fliter multiple fluids mid-pipe? Multiple cover filters and some extra nonuple pipe?

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