Let's say I have an Altaria, and I send it out against a Primal Groudon. It's faster and Desolate Land activates, which Altaria proceeds to shut down with Cloud Nine. If she was to Mega Evolve, would the effects of Desolate Land return?
The effects of harsh sun will come back. Cloud Nine only blocks the effects in a similar manner to Magic Guard; it doesn't make the weather itself go away unfortunately.
Source.(The question is bit different in source but the ans is same)