In one embodiment of the present invention, an encode validator identifies and classifies errors introduced during the parallel chunk-based translation of a source to a corresponding aggregate encode. In operation, upon receiving a source for encoding, a frame difference generator creates a frame difference file for the source. A parallel encoder then distributes per-chunk encoding operations across machines and creates an aggregate encode. The encode validator decodes the aggregate encode and creates a corresponding frame difference file. Subsequently, the encode validator performs phase correlation operations between the two frame difference files to detect errors generated by encoding process faults (i.e., dropping a frame, etc.) while suppressing discrepancies inherent in encoding, such as those attributable to low bit-rate encoding. Advantageously, since the encode validator leverages frame difference files, this indirect verification technique enables efficient debugging of parallel encoding processes in which the complete source is unavailable for post-encode analysis.