diff --git a/crates/omnigraph/src/db/omnigraph.rs b/crates/omnigraph/src/db/omnigraph.rs
index 66a510e..842248f 100644
--- a/crates/omnigraph/src/db/omnigraph.rs
+++ b/crates/omnigraph/src/db/omnigraph.rs
@@ -1497,6 +1497,7 @@ fn json_value_from_array(array: &dyn Array, row: usize) -> Result<serde_json::Va
 #[cfg(test)]
 mod tests {
     use super::*;
+    use crate::db::is_internal_run_branch;
     use crate::db::manifest::ManifestCoordinator;
     use async_trait::async_trait;
     use omnigraph_compiler::{SchemaMigrationStep, SchemaTypeKind};
@@ -1942,6 +1943,47 @@ edge WorksAt: Person -> Company
         );
     }
 
+    #[tokio::test]
+    async fn test_apply_schema_succeeds_after_load_creates_published_run_branch() {
+        // Regression for MR-670: schema apply used to fail after any load or
+        // change because published __run__ branches count as "non-main" in
+        // the blocking-branch check, and there is no CLI path to clean them
+        // up (branch_delete rejects internal refs; run abort rejects
+        // Published runs). Published run branches are intentionally retained
+        // for post-publish inspection — schema apply now filters them out
+        // instead of requiring their deletion.
+        let dir = tempfile::tempdir().unwrap();
+        let uri = dir.path().to_str().unwrap();
+        let mut db = Omnigraph::init(uri, TEST_SCHEMA).await.unwrap();
+
+        // A load goes through a __run__ branch which remains after publish.
+        crate::loader::load_jsonl(
+            &mut db,
+            r#"{"type": "Person", "data": {"name": "Alice", "age": 30}}"#,
+            crate::loader::LoadMode::Overwrite,
+        )
+        .await
+        .unwrap();
+
+        // Confirm at the coordinator level that a published run branch did
+        // get created and persists after publish.
+        let all_branches = db.coordinator.all_branches().await.unwrap();
+        assert!(
+            all_branches.iter().any(|b| is_internal_run_branch(b)),
+            "expected at least one internal run branch after load, got: {:?}",
+            all_branches
+        );
+
+        // Schema apply should succeed — the filter skips internal system
+        // branches, including __run__ ones.
+        let desired = TEST_SCHEMA.replace(
+            "    age: I32?\n}",
+            "    age: I32?\n    nickname: String?\n}",
+        );
+        let result = db.apply_schema(&desired).await.unwrap();
+        assert!(result.applied, "schema apply should have applied");
+    }
+
     #[tokio::test]
     async fn test_apply_schema_adds_index_for_existing_property() {
         let dir = tempfile::tempdir().unwrap();
diff --git a/crates/omnigraph/src/db/omnigraph/schema_apply.rs b/crates/omnigraph/src/db/omnigraph/schema_apply.rs
index 17adc60..bda47e1 100644
--- a/crates/omnigraph/src/db/omnigraph/schema_apply.rs
+++ b/crates/omnigraph/src/db/omnigraph/schema_apply.rs
@@ -32,9 +32,13 @@ pub(super) async fn apply_schema_with_lock(
 ) -> Result<SchemaApplyResult> {
     db.ensure_schema_state_valid().await?;
     let branches = db.coordinator.all_branches().await?;
+    // Skip `main`, the schema-apply lock branch, and any internal `__run__`
+    // branches. Stale run branches used to block schema apply forever after
+    // a publish (MR-670); the publish path now cleans them up, but this
+    // filter is defense-in-depth for legacy repos that predate the fix.
     let blocking_branches = branches
         .into_iter()
-        .filter(|branch| branch != "main" && !is_schema_apply_lock_branch(branch))
+        .filter(|branch| branch != "main" && !is_internal_system_branch(branch))
         .collect::<Vec<_>>();
     if !blocking_branches.is_empty() {
         return Err(OmniError::manifest_conflict(format!(
@@ -369,7 +373,7 @@ pub(super) async fn acquire_schema_apply_lock(db: &mut Omnigraph) -> Result<()>
         .all_branches()
         .await?
         .into_iter()
-        .filter(|branch| branch != "main" && !is_schema_apply_lock_branch(branch))
+        .filter(|branch| branch != "main" && !is_internal_system_branch(branch))
         .collect::<Vec<_>>();
     if !blocking_branches.is_empty() {
         let _ = release_schema_apply_lock(db).await;