I've decided to report this as a bug. I have not seen any mention of this anywhere.
Exalted Angel destiny. Reborn in the light ability. The counter for this disappears when going through a Ddoor, portal, or other means to travel through a quest that requires a loading screen. Through the portal open is a good example where you go through portals to travel. The counter for this goes away each time you have to move to a different hall and you go through the portal.
I don't know if this is WAI, I have not seen any mention of this anywhere so I will be bug reporting this because it is a very stupid thing to have happen to the counter, especially since you need to get it to 100 AND has a 26 minute cool down AND only lasts 2 minutes.