diff --git a/backend/src/app/seeds/loader.py b/backend/src/app/seeds/loader.py
index efa1730..4b47db9 100644
--- a/backend/src/app/seeds/loader.py
+++ b/backend/src/app/seeds/loader.py
@@ -1,11 +1,12 @@
 """Database upsert helpers for seed data."""
 
-from sqlalchemy import delete, select
+from sqlalchemy import delete, select, update
 from sqlalchemy.dialects.postgresql import insert
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from app.models.boss_battle import BossBattle
 from app.models.boss_pokemon import BossPokemon
+from app.models.encounter import Encounter
 from app.models.evolution import Evolution
 from app.models.game import Game
 from app.models.pokemon import Pokemon
@@ -195,17 +196,33 @@ async def upsert_routes(
             for child in route.get("children", []):
                 seed_names.add(child["name"])
 
-        pruned = await session.execute(
-            delete(Route)
-            .where(
+        # Find stale route IDs, excluding routes with user encounters
+        in_use_subq = select(Encounter.route_id).distinct().subquery()
+        stale_route_ids_result = await session.execute(
+            select(Route.id).where(
                 Route.version_group_id == version_group_id,
                 Route.name.not_in(seed_names),
+                Route.id.not_in(select(in_use_subq)),
             )
-            .returning(Route.id)
         )
-        pruned_count = len(pruned.all())
-        if pruned_count:
-            print(f"    Pruned {pruned_count} stale route(s)")
+        stale_route_ids = [row.id for row in stale_route_ids_result]
+
+        if stale_route_ids:
+            # Delete encounters referencing stale routes (no DB-level cascade)
+            await session.execute(
+                delete(RouteEncounter).where(
+                    RouteEncounter.route_id.in_(stale_route_ids)
+                )
+            )
+            # Nullify boss battle references to stale routes
+            await session.execute(
+                update(BossBattle)
+                .where(BossBattle.after_route_id.in_(stale_route_ids))
+                .values(after_route_id=None)
+            )
+            # Now safe to delete the routes
+            await session.execute(delete(Route).where(Route.id.in_(stale_route_ids)))
+            print(f"    Pruned {len(stale_route_ids)} stale route(s)")
 
         await session.flush()