diff --git a/crates/engine/src/lib.rs b/crates/engine/src/lib.rs
index a6243e44f..5f3593ac4 100644
--- a/crates/engine/src/lib.rs
+++ b/crates/engine/src/lib.rs
@@ -757,15 +757,17 @@ impl Session {
         true
     }
 
-    /// Drop selections that no longer exist.
+    /// Drop selections that no longer exist. Every comp keeps its own layer selection (After
+    /// Effects), so selections in comps that are not open survive; only ids that are gone from
+    /// every comp are dropped (#1001).
     pub fn sanitize_state(&mut self) {
         let p = self.project.clone();
         self.state.open_comps.retain(|c| p.comp(*c).is_some());
         if self.state.active_comp.is_some_and(|c| p.comp(c).is_none()) {
             self.state.active_comp = self.state.open_comps.first().copied();
         }
-        if let Some(c) = self.active_comp() {
-            let ids: Vec<LayerId> = c.layers.iter().map(|l| l.id).collect();
+        {
+            let ids: Vec<LayerId> = p.comps().flat_map(|(_, c)| c.layers.iter().map(|l| l.id)).collect();
             self.state.selected_layers.retain(|l| ids.contains(l));
             self.state.selected_props.retain(|(l, _)| ids.contains(l));
             self.state.selected_keys.retain(|k| ids.contains(&k.layer));
diff --git a/crates/script/src/tests.rs b/crates/script/src/tests.rs
index 303bd820a..c18faee71 100644
--- a/crates/script/src/tests.rs
+++ b/crates/script/src/tests.rs
@@ -698,6 +698,36 @@ fn group_selected_false_deselects_masks_and_effects() {
     assert_eq!(out.result, json!([[true, true], [false, true], [false, false]]));
 }
 
+/// A layer selected by script in a comp that is not open stays selected for the next script:
+/// every comp keeps its own layer selection (#1001).
+#[test]
+fn layer_selection_in_a_closed_comp_survives_to_the_next_script() {
+    let mut s = session();
+    let out = ok(
+        &mut s,
+        r#"
+        var a = app.project.items.addComp("Active", 400, 300, 1, 2, 25);
+        a.openInViewer();
+        var c = app.project.items.addComp("Other", 400, 300, 1, 2, 25);
+        c.layers.addText("A");
+        c.layers.addText("B");
+        c.layer("B").selected = true;
+        c.selectedLayers.length + " " + c.layer("B").selected
+        "#,
+    );
+    assert_eq!(out.result, json!("1 true"));
+    // A second script call, the way a panel talks to the app over the control channel.
+    let out = ok(
+        &mut s,
+        r#"
+        var c = null;
+        for (var k = 1; k <= app.project.numItems; k++) { if (app.project.item(k).name === "Other") c = app.project.item(k); }
+        c.selectedLayers.length + " " + c.layer("B").selected
+        "#,
+    );
+    assert_eq!(out.result, json!("1 true"));
+}
+
 /// Probes every file as a 64x32 still (the media layer's single-file probe).
 struct Stills;
 impl effectcraft_engine::Importer for Stills {