So the problem is that two cutscenes - surveillance camera one and elevator one - sets variable chapEnd to 3, and it keeps being 3 afterwards, unless you change it by using workbench/journal/pausemenu. So I fixed it by altering isLoading function by

replacing

current.chapEnd == 3

with

(current.chapEnd == 3 && current.IGT == old.IGT)

Looks not too pretty but it works.

So in 3-1 before bossfight timer does not resume after cutscene with surveillance camera on Neil. So it is paused until chapter ends. Using the thing LiveSplit gets automatically - "Resident%20Evil%20Revelations%202%20Autosplitter%202.asl" by TheDementedSalad.