diff --git a/crates/settings/src/store.rs b/crates/settings/src/store.rs
--- a/crates/settings/src/store.rs
+++ b/crates/settings/src/store.rs
@@ -385,6 +385,13 @@ impl<T: Settings> SettingsStore<T> {
             Err(e) if e.kind() == io::ErrorKind::NotFound => return Ok(None),
             Err(e) => return Err(e.into()),
         };
+        // A blank file still parses, so adopting it below would replace this store's document --
+        // and with it every comment and unknown key the app does not manage -- with an empty one;
+        // blank text is never written as a backup either, so the content would be lost. A blank
+        // file is not an edit to adopt: keep what this store loaded and leave the file alone.
+        if text.trim().is_empty() {
+            return Ok(None);
+        }
         let Ok(mut doc) = document::parse(&text) else {
             self.moved_aside.push(recovery::move_aside(path)?);
             return Ok(None);
diff --git a/crates/settings/tests/recovery.rs b/crates/settings/tests/recovery.rs
--- a/crates/settings/tests/recovery.rs
+++ b/crates/settings/tests/recovery.rs
@@ -178,3 +178,22 @@ fn outside_file_with_failing_migration_is_not_overwritten() {
     assert_eq!(read_config(tmp.path()), external, "the outside file is left untouched");
     assert!(matches!(store.tick(std::time::Instant::now()).status, craft_settings::SaveStatus::Idle), "no retries once read-only");
 }
+
+#[test]
+fn an_emptied_file_is_not_adopted_over_the_loaded_document() {
+    let tmp = tempfile::tempdir().unwrap();
+    write_config(tmp.path(), "schema_version = 2\n\n# my note\n[plugins]\nenabled = true\n\n[general]\nlanguage = \"de\"\n");
+    let (mut store, _) = open_in(tmp.path());
+    store.update(|p| p.general.language = "fr".into());
+    store.flush().unwrap();
+
+    // Emptied while the app runs: an editor crash, a sync tool, a hand `truncate`.
+    write_config(tmp.path(), "");
+    store.update(|p| p.general.language = "es".into());
+    store.flush().unwrap();
+
+    let text = read_config(tmp.path());
+    assert!(text.contains("# my note"), "{text}");
+    assert!(text.contains("[plugins]"), "{text}");
+    assert!(text.contains("language = \"es\""), "{text}");
+}