Espero que o SyncToy não consiga fazê-lo.
Talvez você deva configurar um software de controle de versão para rastrear alterações diferenciais de sua imagem.
Não estou muito familiarizado com este tópico, mas encontrei um artigo em que o aconselho a crie um disco rígido virtual (VHD) com o seu SO simples e faça um segundo VHD com todos os arquivos "diferentes". Então tudo que você precisa fazer é sincronizar o disco secundário, que deve ser muito menor.
Eu recomendo seguir o link, pois explica claramente o que você pode fazer e por que é uma boa ideia. Além disso, quando você está procurando uma maneira de emagrecer seu VHD primário, leia a postagem de Jeff @ Coding Horror: Criando Menor Máquinas Virtuais
Right off the bat, a post by Roy Osherove pointed me in the right direction: How to use Virtual PC and still save lots of room: differencing disks. The concept is similar to backup strategies. What you are doing is creating a "base" VPC and install the most common things that you'll use in almost all situations. Then after prep'ing it, you create a new virtual hard drive (*.VHD file), mark it as a differencing disk, and continue installing additional apps onto this disk. The differencing disk contains the "different" part between the two VHD files. So what have you gained?
Drive space: if you have have two VPC's that each take up 7GB, you're consuming 14GB (I ~really~ hope you didn't just learn something). But if you have a base disk that is 3GB, containing the core of all your VPCs, and two differencing disks, each taking up 4GB, you're now only consuming 11GB. Sure, this may only be a 23% increase in disk space, but consider that this is only two VPCs. Factor in 3 VPCs, and you're now saving 7GB or 33%. The more VPCs, the more space you save, but obviously the law of diminishing returns is in full effect.
Speed of running up a new VPC: if you created every VPC from scratch, you'd have to go through the OS install, not to mention hotfixes and extra components (like a web server, directory service, etc) as well as any core applications every single time you need a new VPC. I've left out that installing an OS in a VPC (before you install the Virtual Machine Additions) is a SLOW process... much slower than on a physical machine. But, if you used differencing disks, you only have to build your OS with the core components, service packs, hotfixes, and core applications one time. Then, when you needed a new VPC, create a new differencing disk, get the latest OS hotfixes, install the apps you need that aren't on your base, and you're hitting the ground running much faster than having to install a new OS.