Fine-tuning object detection (OD) models on combined datasets assumes annotation compatibility, yet datasets often encode conflicting spatial definitions for semantically equivalent categories. We propose an agentic label harmonization workflow that uses a vision-language model to reconcile both category semantics and bounding box granularity across heterogeneous sources before training. We evaluate on document layout detection as a challenging case study, where annotation standards vary widely across corpora. Without harmonization, naïve mixed-dataset fine-tuning degrades a pretrained RT-DETRv2 detector: on SCORE-Bench, which measures how accurately the full document conversion pipeline reproduces ground-truth structure, table TEDS drops from 0.800 to 0.750. Applied to two corpora whose 16 and 10 category taxonomies share only 8 direct correspondences, harmonization yields consistent gains across content fidelity, table structure, and spatial consistency: detection F-score improves from 0.860 to 0.883, table TEDS improves to 0.814, and mean bounding box overlap drops from 0.043 to 0.016. Representation analysis further shows that harmonized training produces more compact and separable post-decoder embeddings, confirming that annotation inconsistency distorts the learned feature space and that resolving it before training restores representation structure.