I've been using windows for 6 months. Shortly I will be adding Gentoo. I will have a dual booting system. Is there a chance that some of my windows files will get lost?

There is a chance if you:

a) resize your windows partition
b) accidently overwrite the windows partition
c) stuff happens...

If you are adding a 2nd hard drive, there should be no problem. If you're resizing, I follow these steps:

1) Backup all important data
2) Run Scandisk, defrag, optimizer in windows
3) Boot a knoppix CD and use QTparted to resize the windows partition, create swap, root, and home partitions (or as many as you want) and a separate Fat32 parition for sharing files between linux and windows
4) reboot into windows just to check to see if it looks like stuff still works
5) reboot and install linux putting GRUB/LILO into the MBR (unless you're using a 3rd party boot loader like XOSL, in which case you want to put GRUB/LILO into the root partition)
6) Cheer when it all works or cry when it fails

If it fails, you kept all your important data and can use your win CD to reinstall windows, then boot into knoppix and fix GRUB/LILO.

There is always a risk of losing stuff at any time, so you should have backups... But I've never actually lost a partition or data doing a multiboot or partition resize...