diff --git a/crates/automation/src/headless.rs b/crates/automation/src/headless.rs
index e9cbca9241..afdceaead5 100644
--- a/crates/automation/src/headless.rs
+++ b/crates/automation/src/headless.rs
@@ -151,8 +151,7 @@ impl Headless {
         // alone (#1547).
         let ext =
             format.map(|f| f.trim_start_matches('.').to_ascii_lowercase()).or_else(|| target.extension().map(|e| e.to_string_lossy().to_ascii_lowercase()));
-        let layered = matches!(ext.as_deref(), Some("psd" | "psb" | "ora")) || ext.as_deref() == Some(photocraft_format::EXTENSION);
-        if layered {
+        if ext.as_deref().is_some_and(file_cmds::layered_extension) {
             // Saving by index must not retarget the next automation command.
             let previously_active = self.session.active_index();
             self.session.set_active(i);
diff --git a/crates/engine/src/file_cmds.rs b/crates/engine/src/file_cmds.rs
index d75cd64504..2d30b35d69 100644
--- a/crates/engine/src/file_cmds.rs
+++ b/crates/engine/src/file_cmds.rs
@@ -152,7 +152,14 @@ pub fn extension(path: &str) -> Option<String> {
 /// Whether a save without a new path may write back to `path`: only layered files (PSD, PSB,
 /// .pcraft). A flat file goes through Save As instead, so it is never flattened over the original.
 pub fn saves_in_place(path: &str) -> bool {
-    extension(path).is_some_and(|ext| matches!(ext.as_str(), "psd" | "psb" | "pcraft" | "ora"))
+    extension(path).is_some_and(|ext| layered_extension(&ext))
+}
+
+/// Whether the lower-case extension `ext` names a layered document format (PSD, PSB, OpenRaster,
+/// .pcraft). A save to one becomes the document's file; any other format is a copy for automation
+/// saves, desktop and headless alike (#1547, #2579).
+pub fn layered_extension(ext: &str) -> bool {
+    matches!(ext, "psd" | "psb" | "pcraft" | "ora")
 }
 
 /// Whether `path` names a document template (.psdt). A template opens as a new untitled document
diff --git a/crates/ui-egui/src/control.rs b/crates/ui-egui/src/control.rs
index ef399809ee..acb42bb016 100644
--- a/crates/ui-egui/src/control.rs
+++ b/crates/ui-egui/src/control.rs
@@ -1772,6 +1772,9 @@ mod tests {
         let r = call(&mut app, &ctx, "app.save", json!({"path": "out.png"}));
         assert_eq!(r["result"], json!({"path": "out.png", "warnings": ["Layers were flattened"]}), "{r}");
         assert_eq!(*written.borrow(), vec!["out.png".to_string()]);
+        // A flat export is a copy: the document keeps its name and file (#2579).
+        let st = app.session.active().unwrap();
+        assert_eq!((st.doc.name.as_str(), st.path.as_deref()), ("warn.psd", Some("in/warn.psd")));
         // Without `path`, only a layered file is written back, like File › Save (#416).
         call(&mut app, &ctx, "app.open", json!({"path": "in/flat.jpg"}));
         let r = call(&mut app, &ctx, "app.save", json!({}));
diff --git a/crates/ui-egui/src/file_dialog/tests.rs b/crates/ui-egui/src/file_dialog/tests.rs
index b0c356ada3..3be31dace7 100644
--- a/crates/ui-egui/src/file_dialog/tests.rs
+++ b/crates/ui-egui/src/file_dialog/tests.rs
@@ -144,7 +144,8 @@ fn layered_save_respects_explicit_jpeg_choices() {
     answer(&open, Some(FileDialogAnswer::SaveTo("/exports/chosen.JPEG".into())));
     app.poll_file_dialog(&ctx, None);
     assert_eq!(*written.borrow(), ["/exports/chosen.jpeg"]);
-    assert_eq!(app.session.active().unwrap().path.as_deref(), Some("/exports/chosen.jpeg"));
+    // The JPEG can't hold the layers, so it is a copy and the document keeps its file (#2550).
+    assert_eq!(app.session.active().unwrap().path.as_deref(), Some("/pics/My image.JPEG"));
     // Explicit command paths carry the same choice and bypass the picker.
     for command in ["file.save", "file.saveAs"] {
         let (mut app, open, written) = jpeg_app(Some("/pics/My image.JPEG"), true);
diff --git a/crates/ui-egui/src/lib.rs b/crates/ui-egui/src/lib.rs
index d0046a3135..17fb5cfdd0 100644
--- a/crates/ui-egui/src/lib.rs
+++ b/crates/ui-egui/src/lib.rs
@@ -210,6 +210,29 @@ impl Default for ExportSettings {
     }
 }
 
+/// The document's lone layer when it is a plain raster a flat file keeps: visible, at full
+/// opacity, in Normal mode, with no masks, effects or blending restrictions (#2234).
+pub(crate) fn plain_raster(doc: &Document) -> Option<&photocraft_doc::Layer> {
+    match doc.layers.as_slice() {
+        [layer]
+            if matches!(layer.content, photocraft_doc::LayerContent::Raster(_))
+                && layer.visible
+                && layer.opacity >= 1.0
+                && layer.fill_opacity >= 1.0
+                && layer.mask.is_none()
+                && layer.vector_mask.is_none()
+                && layer.effects.items.is_empty()
+                && layer.effects.psd_raw.is_none()
+                && matches!(layer.blend, photocraft_color::BlendMode::Normal | photocraft_color::BlendMode::PassThrough)
+                && photocraft_compose::channel_weights(layer, doc.mode).is_none()
+                && !photocraft_compose::blend_if_active(layer, doc.mode) =>
+        {
+            Some(layer)
+        }
+        _ => None,
+    }
+}
+
 /// Encode a document: (file bytes, warnings about anything approximated or dropped).
 pub type ExportFn = Box<dyn Fn(&Document, &str, &ExportSettings) -> Result<(Vec<u8>, Vec<String>), String>>;
 pub type WriteFn = Box<dyn FnMut(&str, &[u8]) -> Result<(), String>>;
@@ -1029,18 +1052,11 @@ impl PhotocraftApp {
         // Other files keep their format only when it can retain their layers. A plain raster
         // (including an unlocked transparent PNG) can keep its flat format; editable contents,
         // masks and layer appearance settings need a layered format even with just one layer.
-        let plain_raster = matches!(st.doc.layers.as_slice(), [layer]
-            if matches!(layer.content, photocraft_doc::LayerContent::Raster(_))
-                && layer.visible && layer.opacity >= 1.0 && layer.fill_opacity >= 1.0
-                && layer.mask.is_none() && layer.vector_mask.is_none()
-                && layer.effects.items.is_empty() && layer.effects.psd_raw.is_none()
-                && matches!(layer.blend, photocraft_color::BlendMode::Normal | photocraft_color::BlendMode::PassThrough)
-                && photocraft_compose::channel_weights(layer, st.doc.mode).is_none()
-                && !photocraft_compose::blend_if_active(layer, st.doc.mode));
+        let flat = plain_raster(&st.doc).is_some();
         let ext = st.path.as_deref().and_then(|p| std::path::Path::new(p).extension()).map(|e| e.to_string_lossy().to_ascii_lowercase());
         let writable = ext.is_some_and(|e| {
             matches!(e.as_str(), photocraft_format::EXTENSION | "psd" | "psb" | "tif" | "tiff" | "ora")
-                || (plain_raster && photocraft_codecs::from_extension(&e).is_some_and(|f| f.caps().write))
+                || (flat && photocraft_codecs::from_extension(&e).is_some_and(|f| f.caps().write))
         });
         let suggested = match &st.path {
             Some(p) if writable => p.clone(),
@@ -1062,7 +1078,14 @@ impl PhotocraftApp {
             tiff_options_ui::park(self, path.clone())?;
             return Ok(serde_json::json!({"path": path, "warnings": []}));
         }
-        match self.write_document(path.clone(), &ExportSettings::default(), false)? {
+        // A flat file that can't hold the document (its layers, or the layered file it lives in)
+        // is written as a copy, as in Photoshop: the document keeps its file, so Save still
+        // writes the layered original and the edits stay unsaved (#2550).
+        let st = self.session.active().ok_or("no document")?;
+        let layered =
+            |p: &str| photocraft_engine::file_cmds::saves_in_place(p) || matches!(photocraft_engine::file_cmds::extension(p).as_deref(), Some("tif" | "tiff"));
+        let copy = !layered(&path) && (plain_raster(&st.doc).is_none() || st.path.as_deref().is_some_and(layered));
+        match self.write_document(path.clone(), &ExportSettings::default(), copy)? {
             Some((path, warnings)) => Ok(serde_json::json!({"path": path, "warnings": warnings})),
             None => Ok(serde_json::json!({"path": path, "warnings": [], "pending": true, "job": self.jobs.last_started.map(|j| j.0)})),
         }
@@ -1134,7 +1157,11 @@ impl PhotocraftApp {
         let (bytes, warnings) = export(&state.doc, &target, &ExportSettings::default())?;
         let write = self.services.automation_write.as_mut().ok_or("automation write authority is not configured")?;
         write(&target, &bytes)?;
-        if let Some(state) = self.session.active_mut() {
+        // Only a layered save becomes the document's file; a flat one is a copy, as in the
+        // headless server (#2579).
+        if photocraft_engine::file_cmds::extension(&target).is_some_and(|e| photocraft_engine::file_cmds::layered_extension(&e))
+            && let Some(state) = self.session.active_mut()
+        {
             state.saved_to(target.clone());
         }
         self.ui.status = format!("Saved {target}");
diff --git a/crates/ui-egui/src/save_identity_tests.rs b/crates/ui-egui/src/save_identity_tests.rs
index f5513a1854..9cfc86d500 100644
--- a/crates/ui-egui/src/save_identity_tests.rs
+++ b/crates/ui-egui/src/save_identity_tests.rs
@@ -116,3 +116,69 @@ fn web_download_and_automation_saves_use_the_same_identity_completion() {
     app.save_automation(Some("保存/agent save.psd".into())).unwrap();
     assert_eq!(app.session.active().unwrap().doc.name, "agent save.psd");
 }
+
+/// Save As to a flat format writes a copy when the flat file can't hold the document: its layers,
+/// or the layered file it already lives in. The document keeps its file, so Save still writes the
+/// layered original and the edits stay unsaved (#2550).
+#[test]
+fn save_as_flat_keeps_the_layered_original() {
+    let ctx = egui::Context::default();
+    // A layered document, and a one-layer one (the issue's case: the dialog offered a JPEG).
+    for layered in [true, false] {
+        let mut app = app();
+        if !layered {
+            app.run("file.new", json!({"width": 4, "height": 4, "name": "Untitled-2"})).unwrap();
+        }
+        let written = Rc::new(RefCell::new(Vec::new()));
+        let w = written.clone();
+        app.services.write = Some(Box::new(move |path, _| {
+            w.borrow_mut().push(path.to_string());
+            Ok(())
+        }));
+        menus::invoke(&mut app, &ctx, "file.saveAs", json!({"path": "art.psd"})).unwrap();
+        app.run("edit.fill", json!({"color": "#000000"})).unwrap();
+        let before = identity(&app);
+        for flat in ["art.jpg", "art.png"] {
+            menus::invoke(&mut app, &ctx, "file.saveAs", json!({"path": flat})).unwrap();
+            assert_eq!(identity(&app), before, "{flat}, layered: {layered}");
+        }
+        menus::invoke(&mut app, &ctx, "file.save", json!({})).unwrap();
+        assert_eq!(*written.borrow(), ["art.psd", "art.jpg", "art.png", "art.psd"]);
+        let st = app.session.active().unwrap();
+        assert_eq!(st.saved_revision, st.revision);
+    }
+    // An untitled layered document saved as a JPEG is still untitled and unsaved.
+    let mut app = app();
+    let before = identity(&app);
+    app.save_as(Some("flat.jpg".into())).unwrap();
+    assert_eq!(identity(&app), before);
+}
+
+/// A flat document that isn't in a layered file becomes the flat file it is saved as, as before.
+#[test]
+fn save_as_flat_retargets_a_flat_document() {
+    let mut app = app();
+    app.run("file.new", json!({"width": 4, "height": 4, "name": "Untitled-2"})).unwrap();
+    app.save_as(Some("shot.png".into())).unwrap();
+    assert_eq!(app.session.active().unwrap().path.as_deref(), Some("shot.png"));
+    app.save_as(Some("shot.jpg".into())).unwrap();
+    let st = app.session.active().unwrap();
+    assert_eq!((st.doc.name.as_str(), st.path.as_deref()), ("shot.jpg", Some("shot.jpg")));
+    assert_eq!(st.saved_revision, st.revision);
+}
+
+/// `app.save` (control channel, MCP bridge) to a flat format is a copy, as in the headless server
+/// (#1547); only a layered format becomes the document's file (#2579).
+#[test]
+fn automation_flat_save_is_a_copy() {
+    let mut app = app();
+    let before = identity(&app);
+    for flat in ["flat.png", "flat.jpg", "flat.tif"] {
+        app.save_automation(Some(flat.into())).unwrap();
+        assert_eq!(identity(&app), before, "{flat}");
+    }
+    app.save_automation(Some("layers.psd".into())).unwrap();
+    let st = app.session.active().unwrap();
+    assert_eq!((st.doc.name.as_str(), st.path.as_deref()), ("layers.psd", Some("layers.psd")));
+    assert_eq!(st.saved_revision, st.revision);
+}