(Progression = being required by the mod to defeat the bosses in a certain order)
"As soon as you enter TF and either die or leave TF, progression bugs out and it thinks you haven't progressed past the Lich until the next restart." (zourath, DW20)
Multiple people have experienced this bug, including me, and it is indeed very annoying.
So, until the pack makers/TF author/we manage to fix it somehow, the idea is that the progression should be disabled.
That is done by changing this setting in TwilightForest.cfg:
# Enforced progression through Twilight Forest dungeons/areas.