@Chubert There are some bits just need to be flushed out. The easies way is to use the fixparts command. If you reload windows you will end up in the same spot and only have accomplished just burning time.
IF you want to reload windows, use a brand new hard drive or one that has never seen a gpt format. That is the way around this issue.
You may be able to clean the disk (destructively) using this process. I say “may” because I haven’t done this route I use fixparts. https://technet.microsoft.com/en-us/library/cc725797(v=ws.11).aspx The downside is that you will have to reload windows and recreate your reference image.