Do you mean catch tank or breather? We don't have a catch tank as standard, just the separator in the breather system which should drain back to the sump.
At a guess, the pipe that goes to the inlet system would now go to the catch tank and it would collect anything. Not sure why it would have two connections tho unless it does vent back to the inlet :? it should be the last thing in the system.
What make is it?