Complex designs generated from modern high-level synthesis tools allow users to take advantage of heterogeneous systems, splitting the execution of programs between conventional processors, and hardware accelerators. While modern HLS tools continue to improve in efficiency and capability, debugging these designs has received relatively minor attention. Fortunately, recent academic work has provided the first means to debug these designs using hardware and software traces. Though these traces allow the user to analyze the flow of execution on both the software and hardware individually, they provide no means of synchronization to determine how operations on one device affect the other. We address this challenge by introducing a synchronization technique that keeps track of operations on shared objects. We identify objects shared between hardware and software and their memory operations, and use unique identifiers to synchronize the traces around these operations. We explore the added costs of this technique on execution time and hardware and software resources, and ways to reduce it through multiple synchronization schemes. This is demonstrated in an open-source prototype targeting the hybrid flow of the open-source HLS-tool LegUp.