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My theory on Dharma food drops is that they come from an alternate timeline in which the Dharma Initiative still exists.
If Jack's plan works and the bomb did go off, then everyone is killed and those who were evactuated from the island likely returned to continue Dharma's work. If the others, including Ben, Widmore etc.. died, then there would be no purge. Maybe Dharma's funding was not cut off and they continued to 2004.