Research on inconsistency-tolerant query answering usually assumes that the terminological knowledge is correct, and only the facts (ABox) need to be repaired. In this paper we study the problem of answering instance queries over inconsistent ontologies, by repairing the whole knowledge base (KB). Contrary to ABox repairs, when KB repairs are considered, instance checking in DL-LiteHorn w.r.t. the brave semantics remains tractable, and the intersection semantics allow for an anytime algorithm. We also show that inconsistency-tolerant instance checking w.r.t. ABox repairs is intractable even if only polynomially many ABox repairs exist.