diff --git a/examples/text_embedding/main.py b/examples/text_embedding/main.py
index 07e83f031..af99585a4 100644
--- a/examples/text_embedding/main.py
+++ b/examples/text_embedding/main.py
@@ -6,6 +6,7 @@
 import os
 from numpy.typing import NDArray
 import numpy as np
+from datetime import timedelta
 
 
 @cocoindex.transform_flow()
@@ -38,7 +39,8 @@ def text_embedding_flow(
     Define an example flow that embeds text into a vector database.
     """
     data_scope["documents"] = flow_builder.add_source(
-        cocoindex.sources.LocalFile(path="markdown_files")
+        cocoindex.sources.LocalFile(path="markdown_files"),
+        refresh_interval=timedelta(seconds=5),
     )
 
     doc_embeddings = data_scope.add_collector()
diff --git a/src/execution/source_indexer.rs b/src/execution/source_indexer.rs
index 33b8198e2..5982425b5 100644
--- a/src/execution/source_indexer.rs
+++ b/src/execution/source_indexer.rs
@@ -125,15 +125,39 @@ impl SourceIndexingContext {
             let source_version = SourceVersion::from_current_data(&source_data);
             let processing_sem = {
                 let mut state = self.state.lock().unwrap();
-                let row_state = state.rows.entry(key.clone()).or_default();
-                if row_state
-                    .source_version
-                    .should_skip(&source_version, Some(update_stats.as_ref()))
-                {
-                    return anyhow::Ok(());
+                let touched_generation = state.scan_generation;
+                match state.rows.entry(key.clone()) {
+                    hash_map::Entry::Occupied(mut entry) => {
+                        if entry
+                            .get()
+                            .source_version
+                            .should_skip(&source_version, Some(update_stats.as_ref()))
+                        {
+                            return anyhow::Ok(());
+                        }
+                        let sem = entry.get().processing_sem.clone();
+                        if source_version.kind == row_indexer::SourceVersionKind::NonExistence {
+                            entry.remove();
+                        } else {
+                            entry.get_mut().source_version = source_version.clone();
+                        }
+                        sem
+                    }
+                    hash_map::Entry::Vacant(entry) => {
+                        if source_version.kind == row_indexer::SourceVersionKind::NonExistence {
+                            update_stats.num_deletions.inc(1);
+                            return anyhow::Ok(());
+                        }
+                        let new_entry = SourceRowIndexingState {
+                            source_version: source_version.clone(),
+                            touched_generation,
+                            ..Default::default()
+                        };
+                        let sem = new_entry.processing_sem.clone();
+                        entry.insert(new_entry);
+                        sem
+                    }
                 }
-                row_state.source_version = source_version.clone();
-                row_state.processing_sem.clone()
             };
 
             let permit = processing_sem.acquire().await?;
@@ -183,11 +207,15 @@ impl SourceIndexingContext {
                         }
                     }
                     hash_map::Entry::Vacant(entry) => {
-                        entry.insert(SourceRowIndexingState {
-                            source_version: target_source_version,
-                            touched_generation: scan_generation,
-                            ..Default::default()
-                        });
+                        if target_source_version.kind
+                            != row_indexer::SourceVersionKind::NonExistence
+                        {
+                            entry.insert(SourceRowIndexingState {
+                                source_version: target_source_version,
+                                touched_generation: scan_generation,
+                                ..Default::default()
+                            });
+                        }
                     }
                 }
             }
@@ -277,15 +305,12 @@ impl SourceIndexingContext {
 
         let deleted_key_versions = {
             let mut deleted_key_versions = Vec::new();
-            let mut state = self.state.lock().unwrap();
+            let state = self.state.lock().unwrap();
             for (key, row_state) in state.rows.iter() {
                 if row_state.touched_generation < scan_generation {
                     deleted_key_versions.push((key.clone(), row_state.source_version.ordinal));
                 }
             }
-            for (key, _) in deleted_key_versions.iter() {
-                state.rows.remove(key);
-            }
             deleted_key_versions
         };
         for (key, source_ordinal) in deleted_key_versions {