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I'm using this formula in a Deadline Alert column:
 
IF({Deadline} < NOW(), "Late", IF(IS_SAME({Deadline}, TODAY(), 'day'), "At Risk", "On Time"))
 
I have a separate Status Column to mark tasks Done. Is there a formula to show "Done" (instead of "Late") in the Deadline Alert column when "Done" is selected in Status? 

I think if you put that IF in front of your existing ones it'd work fine:

IF( {Status} = "Done", "Done", IF( {Deadline} < NOW(), "Late", IF( IS_SAME( {Deadline}, TODAY(), 'day' ), "At Risk", "On Time" ) ) )

Thanks so much @TheTimeSavingCo!