diff --git a/src/features/run/EditConfigsDialog.tsx b/src/features/run/EditConfigsDialog.tsx
index 153081698..461c84b96 100644
--- a/src/features/run/EditConfigsDialog.tsx
+++ b/src/features/run/EditConfigsDialog.tsx
@@ -22,13 +22,12 @@ import {
   kindLabel,
   removeConfig,
   upsertConfig,
-  userConfigs,
   validateConfig,
   type ConfigErrors,
 } from "./configs";
 import { importConfigs, importLabel } from "./importConfigs";
 import { targetName } from "./remote";
-import { saveUserConfigs, selectConfig, useRun } from "./store";
+import { saveEditedConfigs, selectConfig, useRun } from "./store";
 import { blankTemplate, COMPOUND, missingParams, newConfigOfType, templateId, typeFor } from "./types";
 import styles from "./Run.module.css";
 import { tx } from "@/platform/i18n";
@@ -305,7 +304,7 @@ function EditConfigsDialog() {
     }
     setSaving(true);
     try {
-      if (dirty) await saveUserConfigs(userConfigs(draft), removedDetectedIds);
+      if (dirty) await saveEditedConfigs(draft, removedDetectedIds);
       if (templatesDirty && templates) await call(commands.runSaveTemplates(templates));
       setRemovedDetectedIds([]);
       setDirty(false);
diff --git a/src/features/run/removal.test.tsx b/src/features/run/removal.test.tsx
index 29a35c2e5..29733e03a 100644
--- a/src/features/run/removal.test.tsx
+++ b/src/features/run/removal.test.tsx
@@ -6,6 +6,8 @@ const ipc = vi.hoisted(() => ({
   runConfigs: vi.fn(),
   runTemplates: vi.fn(async () => ({ status: "ok", data: [] })),
   runImportSources: vi.fn(async () => ({ status: "ok", data: [] })),
+  runWithoutDerived: vi.fn(async (configs: unknown) => ({ status: "ok", data: configs })),
+  runApplySettings: vi.fn(async (configs: unknown) => ({ status: "ok", data: configs })),
 }));
 vi.mock("@/platform/ipc", async (importOriginal) => ({
   ...(await importOriginal<typeof import("@/platform/ipc")>()),
@@ -17,7 +19,7 @@ import type { RunConfig } from "@/platform/ipc";
 import { useProject } from "@/platform/project";
 import { EditConfigsOverlay } from "./EditConfigsDialog";
 import { ConfigChooserOverlay } from "./ConfigChooser";
-import { canDeleteConfig, deleteConfig, loadConfigs, resetRuns, useRun } from "./store";
+import { adoptTemporary, canDeleteConfig, deleteConfig, loadConfigs, resetRuns, useRun } from "./store";
 import { registerBuiltinTypes } from "./types";
 
 const config = (kind = "npm"): RunConfig => ({
@@ -125,3 +127,43 @@ it("Cancel discards a pending detected removal", () => {
   expect(ipc.runSaveConfigs).not.toHaveBeenCalled();
   expect(useRun.getState().configs).toEqual([config()]);
 });
+
+const temporaryOf = () =>
+  JSON.parse(localStorage.getItem("openidea.run.temporary.v2:/test-removal") ?? "[]") as RunConfig[];
+const mainGo: RunConfig = { ...config("go"), id: "go:file:/test-removal/app/main.go", name: "main.go" };
+
+it("removes a temporary configuration from Edit Configurations for good", async () => {
+  adoptTemporary(mainGo);
+  useRun.setState({ editTarget: mainGo.id });
+  render(<EditConfigsOverlay />);
+  fireEvent.click(screen.getByRole("treeitem", { name: "main.go" }));
+  fireEvent.click(screen.getByRole("button", { name: "Remove Configuration" }));
+  fireEvent.click(screen.getByRole("button", { name: "OK" }));
+  await waitFor(() => expect(useRun.getState().editorOpen).toBe(false));
+  // Not a suppressed detection: it was never detected by the backend.
+  expect(ipc.runSaveConfigs).toHaveBeenCalledWith([], []);
+  expect(temporaryOf()).toEqual([]);
+  await act(() => loadConfigs());
+  expect(useRun.getState().configs.map((c) => c.id)).toEqual(["npm:app"]);
+  expect(useRun.getState().temporary).toEqual([]);
+});
+
+it("keeps unedited temporary configurations temporary and saves edited ones", async () => {
+  const goal: RunConfig = { ...config("maven"), id: "maven:goal:pom.xml:test", name: "app [test]", detected: false };
+  const other: RunConfig = {
+    ...config("maven"),
+    id: "maven:goal:pom.xml:verify",
+    name: "app [verify]",
+    detected: false,
+  };
+  adoptTemporary(goal);
+  adoptTemporary(other);
+  useRun.setState({ editTarget: other.id });
+  render(<EditConfigsOverlay />);
+  fireEvent.change(screen.getByRole("textbox", { name: "Name" }), { target: { value: "verify app" } });
+  fireEvent.click(screen.getByRole("button", { name: "OK" }));
+  await waitFor(() => expect(useRun.getState().editorOpen).toBe(false));
+  expect(ipc.runSaveConfigs).toHaveBeenCalledWith([expect.objectContaining({ id: other.id, name: "verify app" })], []);
+  expect(useRun.getState().temporary).toEqual([goal.id]);
+  expect(temporaryOf().map((c) => c.id)).toEqual([goal.id]);
+});
diff --git a/src/features/run/store.ts b/src/features/run/store.ts
index 1d1396781..e91b56297 100644
--- a/src/features/run/store.ts
+++ b/src/features/run/store.ts
@@ -347,10 +347,11 @@ function persistTemporary() {
   const { configs, temporary } = useRun.getState();
   const list = temporary.map((id) => configs.find((c) => c.id === id)).filter((c): c is RunConfig => !!c);
   writeTemporary(root, list);
+  // A rewrite still pending from an earlier call must not bring back what was removed since.
+  const generation = ++persisting;
   if (!list.length || !isTauri()) return;
   // Then rewritten without what settings derived (the project's Maven, JDK, interpreter…), so a
   // later settings change reaches them as it does detected and saved configurations.
-  const generation = ++persisting;
   void call(commands.runWithoutDerived(list))
     .then((kept) => {
       if (generation === persisting && useProject.getState().project?.root === root) writeTemporary(root, kept);
@@ -432,6 +433,30 @@ export async function deleteConfig(id: string): Promise<void> {
   );
 }
 
+/**
+ * Edit Configurations' OK / Apply. A temporary configuration stays temporary unless it was edited
+ * there (then it is saved, as IDEA makes it permanent), and one removed there is forgotten.
+ */
+export async function saveEditedConfigs(draft: readonly RunConfig[], removedDetectedIds: string[] = []): Promise<void> {
+  const { configs, temporary } = useRun.getState();
+  const unchanged = (c: RunConfig) => {
+    const before = configs.find((o) => o.id === c.id);
+    return !!before && JSON.stringify(before) === JSON.stringify(c);
+  };
+  const kept = temporary.filter((id) => draft.some((c) => c.id === id && unchanged(c)));
+  if (kept.length !== temporary.length) {
+    useRun.setState({
+      configs: configs.filter((c) => !temporary.includes(c.id) || kept.includes(c.id)),
+      temporary: kept,
+    });
+    persistTemporary();
+  }
+  await saveUserConfigs(
+    draft.filter((c) => !c.detected && !kept.includes(c.id)),
+    removedDetectedIds,
+  );
+}
+
 /** Persists user configurations and reloads the merged list. */
 export async function saveUserConfigs(user: RunConfig[], removedDetectedIds: string[] = []): Promise<void> {
   user = await Promise.all(