diff --git a/src-tauri/src/commands.rs b/src-tauri/src/commands.rs
index c18ac50..3a39494 100644
--- a/src-tauri/src/commands.rs
+++ b/src-tauri/src/commands.rs
@@ -387,10 +387,14 @@ pub fn get_all_note_titles(state: State<'_, AppState>) -> Result<Vec<NoteTitleEn
     let config = state.config.lock().map_err(|e| e.to_string())?;
     let vault_path = config.active_vault.as_ref().ok_or("No active vault")?;
     let vault = std::path::Path::new(vault_path);
+    let hn_dir = operations::helixnotes_dir(vault_path);
     let mut entries = Vec::new();
 
     for entry in walkdir::WalkDir::new(vault)
         .into_iter()
+        // Cross-platform exclusion (string "/.helixnotes/" checks miss Windows
+        // backslash paths, which leaked .helixnotes/history snapshots in as dupes).
+        .filter_entry(|e| !operations::is_hidden(e.path()) && !e.path().starts_with(&hn_dir))
         .filter_map(|e| e.ok())
     {
         let path = entry.path();
@@ -398,9 +402,6 @@ pub fn get_all_note_titles(state: State<'_, AppState>) -> Result<Vec<NoteTitleEn
             continue;
         }
         let path_str = path.to_string_lossy();
-        if path_str.contains("/.helixnotes/") || path_str.contains("/.trash/") {
-            continue;
-        }
         if path.extension().and_then(|e| e.to_str()) != Some("md") {
             continue;
         }
@@ -449,15 +450,17 @@ pub fn get_graph_data(state: State<'_, AppState>) -> Result<crate::types::GraphD
     let mut seen_paths: HashSet<String> = HashSet::new();
     let mut contents: Vec<String> = Vec::new();
 
+    let hn_dir = operations::helixnotes_dir(vault_path);
     for entry in walkdir::WalkDir::new(vault)
         .into_iter()
+        // Cross-platform exclusion (string "/.helixnotes/" checks miss Windows
+        // backslash paths; is_hidden also covers .stversions/.stfolder/.trash/.git).
+        .filter_entry(|e| !operations::is_hidden(e.path()) && !e.path().starts_with(&hn_dir))
         .filter_map(|e| e.ok())
     {
         let path = entry.path();
         if !path.is_file() { continue; }
         let path_str = path.to_string_lossy().to_string();
-        if path_str.contains("/.helixnotes/") || path_str.contains("/.trash/")
-            || path_str.contains("/.stversions/") || path_str.contains("/.stfolder") { continue; }
         if path.extension().and_then(|e| e.to_str()) != Some("md") { continue; }
         // Skip Syncthing conflict files
         if let Some(name) = path.file_name().and_then(|n| n.to_str()) {
@@ -483,7 +486,8 @@ pub fn get_graph_data(state: State<'_, AppState>) -> Result<crate::types::GraphD
         // Also index by vault-relative path without extension (e.g. "subfolder/note name")
         if let Ok(rel) = path.strip_prefix(vault) {
             let rel_no_ext = rel.with_extension("");
-            let rel_lower = rel_no_ext.to_string_lossy().to_lowercase();
+            // Normalize Windows backslashes so [[folder/note]] links resolve cross-platform.
+            let rel_lower = rel_no_ext.to_string_lossy().replace('\\', "/").to_lowercase();
             relpath_to_idx.entry(rel_lower).or_insert(idx);
         }
 
diff --git a/src-tauri/src/vault/operations.rs b/src-tauri/src/vault/operations.rs
index 9a0156e..cdb99de 100644
--- a/src-tauri/src/vault/operations.rs
+++ b/src-tauri/src/vault/operations.rs
@@ -154,7 +154,7 @@ fn scan_dir_with_count(dir: &Path, vault_root: &str) -> (Vec<NotebookEntry>, usi
     (entries, note_count)
 }
 
-fn is_hidden(path: &Path) -> bool {
+pub(crate) fn is_hidden(path: &Path) -> bool {
     path.file_name()
         .and_then(|n| n.to_str())
         .map(|n| {
@@ -708,17 +708,20 @@ fn update_wikilinks_after_rename(
     new_title: &str,
 ) {
     let vault = Path::new(vault_path);
-    let vault_prefix = format!("{}/", vault_path);
+    let hn_dir = helixnotes_dir(vault_path);
 
-    // Compute vault-relative path refs (without .md) for path-based wikilink refs
-    let old_rel_ref = old_path.strip_prefix(&vault_prefix)
-        .unwrap_or(old_path)
-        .strip_suffix(".md")
-        .unwrap_or(old_path);
-    let new_rel_ref = new_path.strip_prefix(&vault_prefix)
-        .unwrap_or(new_path)
-        .strip_suffix(".md")
-        .unwrap_or(new_path);
+    // Vault-relative path ref (without .md), normalized to forward slashes so it
+    // matches [[folder/note]] wikilinks on Windows (OS paths use backslashes there).
+    let rel_ref = |p: &str| -> String {
+        let rel = Path::new(p)
+            .strip_prefix(vault)
+            .map(|r| r.to_string_lossy().into_owned())
+            .unwrap_or_else(|_| p.to_string())
+            .replace('\\', "/");
+        rel.strip_suffix(".md").unwrap_or(&rel).to_string()
+    };
+    let old_rel_ref = rel_ref(old_path);
+    let new_rel_ref = rel_ref(new_path);
 
     // Check if another note with the same old_title exists in the vault.
     // If so, title-based replacements (rules 1-3) are ambiguous and must be skipped,
@@ -726,6 +729,7 @@ fn update_wikilinks_after_rename(
     // vs. the other note with the same title.
     let title_is_unique = !WalkDir::new(vault)
         .into_iter()
+        .filter_entry(|e| !is_hidden(e.path()) && !e.path().starts_with(&hn_dir))
         .filter_map(|e| e.ok())
         .any(|e| {
             let p = e.path();
@@ -735,10 +739,6 @@ fn update_wikilinks_after_rename(
             if p.extension().and_then(|ext| ext.to_str()) != Some("md") {
                 return false;
             }
-            let p_str = p.to_string_lossy();
-            if p_str.contains("/.helixnotes/") || p_str.contains("/.trash/") {
-                return false;
-            }
             // Check if this note's filename (without .md) matches the old title
             p.file_stem()
                 .and_then(|s| s.to_str())
@@ -748,12 +748,12 @@ fn update_wikilinks_after_rename(
 
     for entry in WalkDir::new(vault)
         .into_iter()
+        .filter_entry(|e| !is_hidden(e.path()) && !e.path().starts_with(&hn_dir))
         .filter_map(|e| e.ok())
     {
         let path = entry.path();
         if !path.is_file() { continue; }
         let path_str = path.to_string_lossy();
-        if path_str.contains("/.helixnotes/") || path_str.contains("/.trash/") { continue; }
         if path.extension().and_then(|e| e.to_str()) != Some("md") { continue; }
         // Skip the renamed note itself
         if *path_str == *new_path { continue; }
diff --git a/src/lib/components/Editor.svelte b/src/lib/components/Editor.svelte
index 64340d1..92be0f9 100644
--- a/src/lib/components/Editor.svelte
+++ b/src/lib/components/Editor.svelte
@@ -1325,7 +1325,10 @@
 	function wikiLinkFolderPath(entry: NoteTitleEntry): string {
 		const vaultRoot = $appConfig?.active_vault;
 		if (!vaultRoot || !entry.path) return '';
-		const rel = entry.path.startsWith(vaultRoot + '/') ? entry.path.slice(vaultRoot.length + 1) : entry.path;
+		// Normalize Windows backslashes so the folder subtitle shows there too.
+		const path = entry.path.replace(/\\/g, '/');
+		const root = vaultRoot.replace(/\\/g, '/');
+		const rel = path.startsWith(root + '/') ? path.slice(root.length + 1) : path;
 		const parts = rel.split('/');
 		// Return parent folder(s), excluding the filename
 		return parts.length > 1 ? parts.slice(0, -1).join('/') + '/' : '';
diff --git a/src/lib/components/GraphView.svelte b/src/lib/components/GraphView.svelte
index bde8ad9..9a0a44f 100644
--- a/src/lib/components/GraphView.svelte
+++ b/src/lib/components/GraphView.svelte
@@ -76,8 +76,10 @@
 	}
 
 	function getFolderKey(path: string): string {
-		const vaultRoot = $appConfig?.active_vault || '';
-		const rel = vaultRoot && path.startsWith(vaultRoot + '/') ? path.slice(vaultRoot.length + 1) : path;
+		// Normalize Windows backslashes so folder grouping/colours work there too.
+		const p = (path || '').replace(/\\/g, '/');
+		const vaultRoot = ($appConfig?.active_vault || '').replace(/\\/g, '/');
+		const rel = vaultRoot && p.startsWith(vaultRoot + '/') ? p.slice(vaultRoot.length + 1) : p;
 		const slash = rel.indexOf('/');
 		return slash >= 0 ? rel.slice(0, slash) : '';
 	}