What is confusing is that it probably did reset the cooldown timer but not to the barrier but instead the second mystery of kirin.

I do coding so I assume they took the easy road and made barrier type mysteries that have a second active act like a second mystery.

For what I understand about coding is that killing intent worked fine as the 2 parts of Sasuke Kirin are technically 2 different Mystery so the second part did reset but the main barrier mystery did not