Well technically the kothringi went extinct in tamriel but there were reports of a ship of uninfected kothringi leaving tamriel leaving the door open to a comeback. The flu also drove the only indigenous humans to extinction in tamriel

Miraak was existing fully in apocrypha while potema was partially summoned.I think it is mentioned a couple of time that if the wolf queen was to fully return it would be catastrophic and wasn't the dragonborn able to stop that process from being completed fully, since she wasn't 100% there no soul