2012 MacBook Pro OS X El Capitan wont boot into windows 8.1 after a HD partition change
Try this:

sudo fdisk -e /dev/disk0
p
setpid 4
07
flag 4
p
write
y


This is assuming that your Boot Camp partition is still active, just not bootable. Reboot, and hold the option key as usual, and see if the bootable partition is available. This will likely fix your issue. 

Just in case it doesn't, this article outlines some steps you can try.