How to repair a flat roof. Depending on the nature and scale of the damage and the type of roofing installed, a flat roof can be repaired in several ways. First identify the source of the leak and locate the damaged area. Prepare the surface for a patch repair on a rubber roof and apply an EPDM patch to a clean, primed surface. Seal cracks in concrete roofing using liquid rubber for the best results. Extensively repaired flat roofing should ideally be removed and replaced.