Converting project fails 4.5- 4.6 github version

I have been using a modded version of 4.5 to develop a game. The mod involves adding a function to the AIController to allow you to abort a currently executing task in a behaviour tree from blueprint. I have attempted to upgrade to 4.6 and copied this mod across successfully. It compiles and runs and I can create a new project perfectly well. However when I attempt to convert my project from 4.5 to 4.6 it comes across the following problems:

The project failed to compile with this version of the engine. Build output is as follows:

Running D:/My Documents/GitHub/UnrealEngine/Engine/Binaries/DotNET/UnrealBuildTool.exe MyProject7 Development Win64 -project="D:/My Documents/GitHub/MyProject7 4.6 - 4/MyProject7.uproject" -editorrecompile -progress
Building UnrealHeaderTool...
Target is up to date.
Parsing headers for MyProject7Editor
Reflection code generated for MyProject7Editor
Failed to delete file 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.pdb'
    Exception: Access to the path 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.pdb' is denied.
Attempting to retry...
Failed to delete file 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.pdb'
    Exception: Access to the path 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.pdb' is denied.
Attempting to retry...
Failed to delete file 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.pdb'
    Exception: Access to the path 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.pdb' is denied.
ERROR: Exhausted all retries!
Performing 23 actions (4 in parallel)
[3/23] Resource ModuleVersionResource.rc.inl
[4/23] Resource MyProject7.rc
Module.UE4Game.cpp
PCH.MyProject7.MyProject7.h.cpp
[5/23] Link UE4Editor-UE4Game.dll
LINK : fatal error LNK1104: cannot open file 'D:\My Documents\GitHub\UnrealEngine\Engine\Binaries\Win64\UE4Editor-UE4Game.dll'
MapChunkBase.cpp
BaseEnemyCode.cpp
MyProject7.generated.cpp
MapSpawner.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\MapChunkBase.cpp(9): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\MapSpawner.cpp(10): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\BaseEnemyCode.cpp(8): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
DoorPin.cpp
EncounterPin.cpp
DetonatorJudge.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\DetonatorJudge.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\EncounterPin.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
ScoreManager.cpp
ScoreJudge.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\ScoreJudge.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\ScoreManager.cpp(8): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.

EnemySpawnPin.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\EnemySpawnPin.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
BPLibrary.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\BPLibrary.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
RemovePauseText.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\RemovePauseText.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
CustomCharacter.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\CustomCharacter.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
DoorBase.cpp
PickupBase.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\DoorPin.cpp(8): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\DoorBase.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
D:\My Documents\GitHub\MyProject7 4.6 - 4\Source\MyProject7\PickupBase.cpp(7): warning C4996: FPostConstructInitializeProperties is deprecated and was renamed to FObjectInitializer. Please use that type instead.
MyProject7.cpp
D:\My Documents\GitHub\MyProject7 4.6 - 4\Intermediate\Build\Win64\Inc\MyProject7\MyProject7.generated.inl(9): warning : .generated.inl files have been deprecated - please remove the associated #include from your code
AutoStartupModuleListGetter.generated.cpp
[23/23] Link UE4Editor-MyProject7.dll
   Creating library D:\My Documents\GitHub\MyProject7 4.6 - 4\Intermediate\Build\Win64\MyProject7Editor\Development\UE4Editor-MyProject7.lib and object D:\My Documents\GitHub\MyProject7 4.6 - 4\Intermediate\Build\Win64\MyProject7Editor\Development\UE4Editor-MyProject7.exp
-------- End Detailed Actions Stats -----------------------------------------------------------
Cumulative action seconds (8 processors): 0.00 building projects, 26.22 compiling, 0.00 creating app bundles, 0.00 generating debug info, 1.26 linking, 0.00 other
UBT execution time: 123.76 seconds

Does anyone know why this might be the case and what I can do to get my project running again?

Well following the solution here I managed to get it working. I guess this can be marked as closed.