My experience with doing this has been that, yes, your Windows partition will continue to function. This has worked for me several times.
However, my most recent experience with doing so has a small problem with switching between the operating systems. I can perform the "option key boot" fine, and selecting the Windows boot icon works perfectly. But if it try to set the "SystemPreferences / StartupDisk" from OS X, I receive a message that "the selected startup disk can't be blessed", and it does not then reboot. I can however, tell OS X to reboot, and use the "option" key to select my Windows boot.
I have Google'd this "blessed disk" issue and found many others with the same message, and almost as many "solutions" to fixing it. I have not yet tried any of them, as it is pretty easy to just use the "option key" and be done with it.
-howard
EDIT: The "blessed disk" issue was created by doing the following:
I had installed a 512GB SSD in my late 2011 MBPro and moved the 750GB hard disk to an optibay. I had been running a DIY Fusion drive without any problems and had the SSD partitioned for Windows and Fusion joined with the hard disk. I decided I wanted to separate the Fusion drives back into separate disks so that I could swap the hard drive and optical drive easily if desired. So I delete the Fusion drive keeping the Windows partition on the SSD intact, and then reinstalled OS X and the recovery partitions on the SSD, and put my media libraries on the hard disk. It is all running fine again other than the "convenience startup disk" selection issue.