Edit & continue not working in VS2015 Update 3 (x64) - c++

Question

After a bit of nightmare getting Vs2015 update 3 installed, as per this related question, I rebuilt my MFC C++ project to see how the update performed only to find Edit and Continue is no longer working! Specifically, making any change to any file and using Debug / Apply Code changes i get the following;
myfile.CPP ......\common\myfile.CPP(1): fatal error C1010: unexpected end of file while looking for precompiled header. Did you
forget to add '#include "\cpp\common\stdafx.h"' to your source?
Project : error (null) : Build errors occurred.
The first include in the source file is
#include "\cpp\common\StdAfx.h"
This worked most of the time under update 2, but edit and continue was failing and reporting that it had succeeded reasonably regularly. Only reason I installed this update as it was supposed to fix this issue but now it is broken entirely and I'm looking at a full uninstall, and re-install of VS2015 update 2 over the weekend.
Anyone else hitting this problem and have a solution? Could possibly be a dodgy installation as even on the full ISO install, the installer failed with missing files and I had to skip two sections. Given this is a release and not a release candidate, the QA seems abysmal, I fail to see why a release version would include any beta functionality. VS2015 detail below;
Microsoft Visual Studio Professional 2015 Version 14.0.25421.03 Update
3 Microsoft .NET Framework Version 4.6.01055
Installed Version: Professional
LightSwitch for Visual Studio 2015 00325-60000-80195-AA437 Microsoft
LightSwitch for Visual Studio 2015
Visual Basic 2015 00325-60000-80195-AA437 Microsoft Visual Basic
2015
Visual C# 2015 00325-60000-80195-AA437 Microsoft Visual C# 2015
Visual C++ 2015 00325-60000-80195-AA437 Microsoft Visual C++ 2015
Application Insights Tools for Visual Studio Package 7.0.20622.1
Application Insights Tools for Visual Studio
ASP.NET and Web Tools 2015.1 (Beta8) 14.1.11106.0 ASP.NET and Web
Tools 2015.1 (Beta8)
ASP.NET Web Frameworks and Tools 2012.2 4.1.41102.0 For additional
information, visit http://go.microsoft.com/fwlink/?LinkID=309563
ASP.NET Web Frameworks and Tools 2013 5.2.40314.0 For additional
information, visit http://www.asp.net/
Common Azure Tools 1.8 Provides common services for use by Azure
Mobile Services and Microsoft Azure Tools.
InstallShield Limited Edition InstallShield. For more information
visit the Flexera Software website at
http://www.FlexeraSoftware.com. Copyright © 2015 Flexera Software
LLC. All Rights Reserved.
JavaScript Language Service 2.0 JavaScript Language Service
JavaScript Project System 2.0 JavaScript Project System
Microsoft Azure Mobile Services Tools 1.4 Microsoft Azure Mobile
Services Tools
PreEmptive Analytics Visualizer 1.2 Microsoft Visual Studio
extension to visualize aggregated summaries from the PreEmptive
Analytics product.
SQL Server Data Tools 14.0.60519.0 Microsoft SQL Server Data Tools
TypeScript 1.8.34.0 TypeScript tools for Visual Studio
Visual Assist For more information about Visual Assist, see the
Whole Tomato Software website at http://www.WholeTomato.com. Copyright
(c) 1997-2016 Whole Tomato Software, Inc.
Visual Commander 2.3 For more information about Visual Commander,
see the website at https://vlasovstudio.com/visual-commander/.
Copyright (c) 2013-2015 Vlasov Studio.
Visual Studio Tools for Universal Windows Apps 14.0.25420.01 The
Visual Studio Tools for Universal Windows apps allow you to build a
single universal app experience that can reach every device running
Windows 10: phone, tablet, PC, and more. It includes the Microsoft
Windows 10 Software Development Kit.
(Apologies for the ranty nature of this question, but I also put it up as a caveat for those thinking of installing this update)

Answer 1

Following on from the same discussion on MSDN here a breaking change in update 3 is as follows
Allow Precompiling (Native only): The debug option Debug > Options >
General > Allow Precompiling (Native only) is no longer supported with
Visual Studio 2015 Update 3 and the default debugger. This is a legacy
setting for a marginal performance improvement that has no functional
impact.
Disabling the above and doing a rebuild all fixes edit and continue.