I upgraded to OS X Mavericks last night, and my BootCamp running Windows 8.1 is just fine. What I did was download the upgrade off the app store, then instead of installing after the download I restarted my computer and held the Option key at the startup. I chose recovery drive. I then erased the OS X Partition and then chose "Install OS X" from the menu. During the install, you have the option to migrate your data from another Mac or from a Time Machine Backup, After my TMB finished installing. Both of my partitions boot perfectly. Not sure if this will help anyone, but this is the route I took when upgrading to ML and my BootCamp partition was untouched then as well.
Also, I went with the install imediately after downloading option first, and after Mavericks installed, I was no longer the administrator for my computer and I wasn't able to boot into Single User Mode to fix it, then I remembered how I did it last year and just started over. Hope this helps!
btw, I have a mid 2010 Macbook Pro, 16GB RAM, 1TB Hybrid SSHD