diff --git a/models/rfd3/src/rfd3/engine.py b/models/rfd3/src/rfd3/engine.py
index 77cbc6f..7d7bd5b 100644
--- a/models/rfd3/src/rfd3/engine.py
+++ b/models/rfd3/src/rfd3/engine.py
@@ -48,9 +48,8 @@ class RFD3InferenceConfig:
     diffusion_batch_size: int = 16
 
     # RFD3 specific
-    skip_existing: bool = False
-    json_keys_subset: Optional[List[str]] = None
     skip_existing: bool = True
+    json_keys_subset: Optional[List[str]] = None
     specification: Optional[dict] = field(default_factory=dict)
     inference_sampler: SampleDiffusionConfig | dict = field(default_factory=dict)
 
@@ -216,6 +215,9 @@ class RFD3InferenceEngine(BaseInferenceEngine):
             inputs=inputs,
             n_batches=n_batches,
         )
+        if len(design_specifications) == 0:
+            ranked_logger.info("No design specifications to run. Skipping.")
+            return None
         ensure_inference_sampler_matches_design_spec(
             design_specifications, self.inference_sampler_overrides
         )
@@ -381,12 +383,18 @@ class RFD3InferenceEngine(BaseInferenceEngine):
     ) -> Dict[str, dict | DesignInputSpecification]:
         # Find existing example IDS in output directory
         if exists(self.out_dir):
-            existing_example_ids = set(
+            existing_example_ids_ = set(
                 extract_example_id_from_path(path, CIF_LIKE_EXTENSIONS)
                 for path in find_files_with_extension(self.out_dir, CIF_LIKE_EXTENSIONS)
             )
+            existing_example_ids = set(
+                [
+                    "_model_".join(eid.split("_model_")[:-1])
+                    for eid in existing_example_ids_
+                ]
+            )
             ranked_logger.info(
-                f"Found {len(existing_example_ids)} existing example IDs in the output directory."
+                f"Found {len(existing_example_ids)} existing example IDs in the output directory ({len(existing_example_ids_)} total)."
             )
 
         # Based on inputs, construct the specifications to loop through
@@ -405,7 +413,6 @@ class RFD3InferenceEngine(BaseInferenceEngine):
             for batch_id in range((n_batches) if exists(n_batches) else 1):
                 # ... Example ID
                 example_id = f"{prefix}_{batch_id}" if exists(n_batches) else prefix
-
                 if (
                     self.skip_existing
                     and exists(self.out_dir)