I just came across this but a team mate said the same thing happened in phase 1 of this summer event with the dark boost.
Normally when we have multiple boosts, in this case the 80% guardian boost and the 30% elemental/epic one, they both apply. Since the breeding event was changed midway with no warning, we now see many epics being bred and they start with a time around 4.5h with both boosts. And that seems to work as intended, unless you need to reload the game, then it appears we lose the 30% boost and now you have to wait a couple extra hours.
I have some before and after screenshots I can post later to show the timing change. Hopefully this can be fixed soon!