About elise:
Maybe the black rose actually has tools to protect them from the black mist?
The new lore talks about a mystical veil protecting the blessed islands,so maybe that veil transformed into the black mist and can still be cleared away with the very same words that kalista used to get to the islands?
Alternatively it is possible that the black mist has its up and down times.
After the harrowing it might disappear for a few weeks/months/whatever completely until it regenerated its power.Karthus merely arrived at a time where the black mist was powerful enough to manifest again.