Grub under normal circumstances wont damage partitions. At worst you would just have to rewrite the Main MBR. grub acts much like the bios would and searches the partition you ask it to boot for normal boot files. when you specify chainloader +1 for windows it searches the partition you specified for files like ntldr or msdos.sys etc that are windows boot files. when you ask it to boot a nix system you tell it the kernel is at /boot/... so it loads that file. Ive installed linux, bsd, solaris... thousands of times on many machines. I have never seen it destroy any thing nor heard of it doing so. theres always a fluke posibility but its far more likely for you to have drive failure that grub to break things.
/etc/grub.d/ is where ubuntu puts the files as well. I suspect grub requires that location.
/etc/grub.d# ls
00_header 10_linux 20_memtest86+ 40_custom README
05_debian_theme 20_linux_xen 30_os-prober 41_custom
Above is a listing of my grub.d/ 40 and 41 are ment for windows partitions etc
the os prober found my primary win partition and added it in your 40_custom would need to be similer to below you would need to use blkid to find the uuid of your win partition to fix the search line and let you change the set root line correctly
menuentry "Microsoft Windows XP Professional (on /dev/sdb1)" --class windows --class os {
insmod part_msdos
insmod ntfs
set root='(/dev/sdb,msdos1)'
search --no-floppy --fs-uuid --set=root D8C0FF3EC0FF2204
drivemap -s (hd0) ${root}
chainloader +1
Above is what it put in to my grub.cfg automagicly. Also fyi if you just have to get win back and will get to linux later using a bartPE or other similer disk. Run a mbr repair utility to set it back to a win mbr. From there you can either use a boot cd/usb drive that has grub on it to boot to the linux partitions. Make sure to copy off the information in the grub.cfg for that linux partition. the live usb drives are very handy that way. they often come with grub installed so you can usually just add to their grub.cfg the lines needed to make a "emergency boot" menu option for linux. just make sure to use uuid's for setting root and such.