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Kenan Sr. was a leader in the Wilmington insurrection of 1898, in which white men marched through town and killed several black men.
Chancellor Carol L. Folt said in a statement Wednesday that the university will now "focus instead on the donor who made the gift, William R. Kenan Jr."
She said the university's History Task Force will also work to tell the "full and complete history" of the Wilmington race riot.
Folt said the decision about the plaques was made after talking with the Kenan family.