Windows will overwrite the existing MBR of yours, rendering your FreeBSD not bootable. Do not worry. As long as you do not erase your FreeBSD partition, all your data and programs are still there!
The easiest way to restore your FreeBSD MBR is use your FreeBSD boot/install disk. Select "standard install" and you can see your FreeBSD system is still there. Just do not "W" any change to it, but "install the FreeBSD MBR" and then exit the installer.
After reboot, you can see Windows and FreeBSD are in the boot menu again.
Next time, remember to back up your data. =D