Matter is still vanishing into the void.
Liquid test chambers after 5 cycles (started with 8*1000kg water):
Gas test chambers after one cycle (started with 36*1000g oxygen):
TL;DR: The issue with disappearing matter inside plumbing is not yet fixed.
Test save file: running tests.sav
Updated title to reflect that it's still happening in the current version.
Load the save, turn on the switches, wait a moment.