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Since they're now immune to disease, they would effectively succeed on any saving throw from that point on, making it go away. Any damage they've taken up until that point from the disease wouldn't instantly go away, so it would need to be removed normally.
Because the immunity counts for magical and supernatural diseases, yes it would do the same for mummy rot, despite the note that it needs remove curse & disease. If you really want for some reason, you can have them technically still have the disease but can't take damage from it, so it wouldn't have any effect.

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Unless I missed something in the description they could still have the damage removed magically (just not naturally) even if you ruled that they still have the non-progressing affliction--they just now technically have a disease while showing no symptoms. Though that gives me an interesting idea for a contagious carrier...
But if I were GM'ing in this situation, I would say that the affliction is cured, magical or no, when the monk hits level 5--more than anything just for simplicity, and because I highly doubt there's an official rule for this situation.