diff --git a/crates/emmylua_code_analysis/src/semantic_db/index/types.rs b/crates/emmylua_code_analysis/src/semantic_db/index/types.rs
index f6e412341..3ad210955 100644
--- a/crates/emmylua_code_analysis/src/semantic_db/index/types.rs
+++ b/crates/emmylua_code_analysis/src/semantic_db/index/types.rs
@@ -51,6 +51,8 @@ impl WorkspaceTypeIndex {
             })
     }
 
+    /// Remove only the given file's definitions, preserving same-name declarations
+    /// from other files even when they share a named semantic ID.
     pub(crate) fn remove_file(&mut self, file_id: FileId) {
         let Some(keys) = self.by_file.remove(&file_id) else {
             return;
@@ -61,7 +63,7 @@ impl WorkspaceTypeIndex {
             };
             let new_defs: Vec<TypeDef> = defs
                 .iter()
-                .filter(|def| def.id != type_id)
+                .filter(|def| def.id != type_id || def.file_id != file_id)
                 .cloned()
                 .collect();
             if new_defs.is_empty() {
diff --git a/crates/emmylua_code_analysis/src/semantic_db/mod.rs b/crates/emmylua_code_analysis/src/semantic_db/mod.rs
index a7c0f61b6..0812ff3b7 100644
--- a/crates/emmylua_code_analysis/src/semantic_db/mod.rs
+++ b/crates/emmylua_code_analysis/src/semantic_db/mod.rs
@@ -17,6 +17,7 @@ pub(crate) mod types;
 pub(crate) mod update;
 
 use hashbrown::{HashMap, HashSet};
+use itertools::Itertools;
 use std::fmt;
 use std::path::PathBuf;
 use std::sync::Arc;
@@ -258,7 +259,9 @@ fn compute_workspace_ids(roots: &[WorkspaceRoot]) -> Vec<WorkspaceId> {
     let mut ids: Vec<WorkspaceId> = if roots.is_empty() {
         vec![WorkspaceId::MAIN]
     } else {
-        roots.iter().map(|root| root.id).collect()
+        // Several roots can belong to the same logical workspace (notably MAIN).
+        // Aggregate each workspace index once, preserving registration order.
+        roots.iter().map(|root| root.id).unique().collect()
     };
     if !ids.contains(&WorkspaceId::REMOTE) {
         ids.push(WorkspaceId::REMOTE);
diff --git a/crates/emmylua_code_analysis/src/semantic_db/phase_tests/p10_tests.rs b/crates/emmylua_code_analysis/src/semantic_db/phase_tests/p10_tests.rs
index 276e2d862..b89f6e066 100644
--- a/crates/emmylua_code_analysis/src/semantic_db/phase_tests/p10_tests.rs
+++ b/crates/emmylua_code_analysis/src/semantic_db/phase_tests/p10_tests.rs
@@ -119,6 +119,65 @@ fn p10_workspace_id_caches_follow_root_changes() {
     assert_eq!(db.workspace_id_of(fid), Some(WorkspaceId::MAIN));
 }
 
+#[test]
+fn p10_multiple_main_roots_do_not_duplicate_type_definitions() {
+    let mut db = setup();
+    let other_root = p10_base().join("other");
+    db.add_main_workspace(other_root.clone());
+    db.add_library_workspace(&WorkspaceFolder::new(p10_library_root(), true));
+    let library_id = db
+        .all_workspace_ids()
+        .iter()
+        .copied()
+        .find(|id| id.is_library())
+        .unwrap();
+    let expected_ids = [WorkspaceId::MAIN, library_id, WorkspaceId::REMOTE];
+    assert_eq!(db.all_workspace_ids(), expected_ids);
+    assert_eq!(db.workspace_lookup_order(), expected_ids);
+
+    let source = "---@class Metrics\nlocal Metrics = {}";
+    let first = set_test_file(&mut db, 1, &p10_main_file("metrics.lua"), source);
+    assert_eq!(db.analysis().type_def_locations(first, "Metrics").len(), 1);
+
+    // Rebuilding indexes after a root change must preserve the same count.
+    db.add_main_workspace(p10_base().join("third"));
+    assert_eq!(db.all_workspace_ids(), expected_ids);
+    assert_eq!(db.workspace_lookup_order(), expected_ids);
+    assert_eq!(db.analysis().type_def_locations(first, "Metrics").len(), 1);
+
+    // A real declaration edit must remove the old name and index the new one.
+    set_test_file(
+        &mut db,
+        1,
+        &p10_main_file("metrics.lua"),
+        &source.replace("Metrics", "RenamedMetrics"),
+    );
+    assert!(
+        db.analysis()
+            .type_def_locations(first, "Metrics")
+            .is_empty()
+    );
+    assert_eq!(
+        db.analysis()
+            .type_def_locations(first, "RenamedMetrics")
+            .len(),
+        1
+    );
+    set_test_file(&mut db, 1, &p10_main_file("metrics.lua"), source);
+    assert!(
+        db.analysis()
+            .type_def_locations(first, "RenamedMetrics")
+            .is_empty()
+    );
+    assert_eq!(db.analysis().type_def_locations(first, "Metrics").len(), 1);
+
+    // Different declarations with the same name still count as duplicates.
+    set_test_file(&mut db, 2, &other_root.join("metrics.lua"), source);
+    assert_eq!(db.analysis().type_def_locations(first, "Metrics").len(), 2);
+    set_test_file(&mut db, 2, &other_root.join("metrics.lua"), "return {}");
+    assert_eq!(db.analysis().type_def_locations(first, "Metrics").len(), 1);
+}
+
 #[test]
 fn p10_type_buckets_share_arc_and_invalidate_on_write() {
     let mut db = setup();