diff --git a/Keybinding.Test/SaveWithoutInitializeTests.cs b/Keybinding.Test/SaveWithoutInitializeTests.cs
index ff09e5d..1359249 100644
--- a/Keybinding.Test/SaveWithoutInitializeTests.cs
+++ b/Keybinding.Test/SaveWithoutInitializeTests.cs
@@ -113,6 +113,75 @@ public async Task SaveAsync_WithoutInitialize_KeepsStoredCommandsAndActiveProfil
 		Assert.AreEqual("file.save", reloaded.Keybindings.ExecuteChord("default", Chord.Parse("Ctrl+S")));
 	}
 
+	[TestMethod]
+	public async Task SaveAsync_TwiceWithoutInitialize_KeepsStoredCommands()
+	{
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			await manager.InitializeAsync().ConfigureAwait(false);
+			manager.Commands.RegisterCommand(new Command("file.save", "Save"));
+			manager.CreateDefaultProfile();
+			manager.Keybindings.BindChord("file.save", Chord.Parse("Ctrl+S"));
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			manager.Profiles.CreateProfile("other", "Other");
+			await manager.SaveAsync().ConfigureAwait(false);
+
+			// The first save carried file.save through; the second must not read it as unregistered here
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		using KeybindingManager reloaded = new(_testDataDirectory);
+		await reloaded.InitializeAsync().ConfigureAwait(false);
+		Assert.IsTrue(reloaded.Commands.IsCommandRegistered("file.save"));
+		Assert.AreEqual("file.save", reloaded.Keybindings.ExecuteChord("default", Chord.Parse("Ctrl+S")));
+	}
+
+	[TestMethod]
+	public async Task SaveAsync_TwiceAfterAnotherManagerSaved_KeepsItsCommand()
+	{
+		using KeybindingManager first = new(_testDataDirectory);
+		using KeybindingManager second = new(_testDataDirectory);
+		await first.InitializeAsync().ConfigureAwait(false);
+		await second.InitializeAsync().ConfigureAwait(false);
+
+		first.Commands.RegisterCommand(new Command("a.cmd", "A"));
+		second.Commands.RegisterCommand(new Command("b.cmd", "B"));
+		second.Profiles.CreateProfile("bprof", "B profile");
+		await second.SaveAsync().ConfigureAwait(false);
+
+		await first.SaveAsync().ConfigureAwait(false);
+		await first.SaveAsync().ConfigureAwait(false);
+
+		using KeybindingManager reloaded = new(_testDataDirectory);
+		await reloaded.InitializeAsync().ConfigureAwait(false);
+		Assert.IsTrue(reloaded.Commands.IsCommandRegistered("a.cmd"));
+		Assert.IsTrue(reloaded.Commands.IsCommandRegistered("b.cmd"));
+		Assert.IsTrue(reloaded.Profiles.ProfileExists("bprof"));
+	}
+
+	[TestMethod]
+	public async Task SaveAsync_CommandUnregisteredAfterItsFirstSave_IsRemovedOnTheNext()
+	{
+		{
+			using KeybindingManager manager = new(_testDataDirectory);
+			manager.Commands.RegisterCommand(new Command("file.save", "Save"));
+			manager.Commands.RegisterCommand(new Command("tools.legacy", "Legacy"));
+			await manager.SaveAsync().ConfigureAwait(false);
+
+			Assert.IsTrue(manager.Commands.UnregisterCommand("tools.legacy"));
+			await manager.SaveAsync().ConfigureAwait(false);
+		}
+
+		using KeybindingManager reloaded = new(_testDataDirectory);
+		await reloaded.InitializeAsync().ConfigureAwait(false);
+		Assert.IsTrue(reloaded.Commands.IsCommandRegistered("file.save"));
+		Assert.IsFalse(reloaded.Commands.IsCommandRegistered("tools.legacy"));
+	}
+
 	[TestMethod]
 	public async Task SaveAsync_CommandUnregisteredByManagerThatLoadedIt_IsRemoved()
 	{
diff --git a/Keybinding/KeybindingManager.cs b/Keybinding/KeybindingManager.cs
index 268a3bf..ff77d97 100644
--- a/Keybinding/KeybindingManager.cs
+++ b/Keybinding/KeybindingManager.cs
@@ -152,7 +152,10 @@ .. storedCommands.Where(c => !commandIds.Contains(c.Id.ToString()) && !_persiste
 		lock (_persistedStateLock)
 		{
 			_persistedCommandIds.Clear();
-			_persistedCommandIds.UnionWith(commandsToSave.Select(c => c.Id.ToString()));
+			// Only the commands registered here count as persisted by this manager. The stored ones it carried through
+			// belong to someone else; marking them too would make the next save read them as unregistered here and
+			// drop them from the file.
+			_persistedCommandIds.UnionWith(commandIds);
 		}
 
 		// Remove stored profiles that were deleted in memory, so they do not come back on the next load. Only