Optical transport networks (OTNs) carry Ethernet traffic over lightpaths that can be provisioned using elastic optical networks (EONs) with flexible spectrum allocation. Under dynamic traffic, frequent client arrivals and departures create scattered free capacity across parallel lightpaths in the transport layer and spectrum fragmentation in the optical layer, leading to underutilized lightpath capacity and spectrum gaps. To quantify and mitigate the transport-layer inefficiency, we introduce a metric called \emph{lightpath utilization entropy} and propose a corresponding \emph{OTN consolidation} strategy that rearranges existing clients across lightpaths serving the same O/D pair to consolidate free capacity. Because this operation is confined to the electrical domain, it can be executed quickly and with minimal service disruption. To jointly address both impairments, we further develop a cross-layer framework that simultaneously consolidates client allocation in the transport layer and reconfigures lightpath placement in the optical layer. We formulate the resulting cross-layer consolidation and defragmentation (CLCD) problem as a cutting-stock model and solve it efficiently by column generation. Because optical-layer reconfiguration is slower, CLCD is executed less frequently than OTN consolidation and is complemented by the latter at a higher frequency. Simulation results demonstrate that the proposed framework, combining CLCD with OTN consolidation, reduces the blocking ratio by up to 51% under medium traffic loads and outperforms single-layer (EON-only) defragmentation in both performance and resource utilization.