Ubuntu fails to boot after windows chkDsk

Basically after a WINDOWS CHKDSK w/ Auto fix on the drive that UBUNTU was located I was unable to boot UBUTU (12.1) again. I would just get the GRUB command prompt. After an extensive research I realized that the WINDOW had deleted my boot.disk without creating a found.000 directory. The problem started with a bug in my shell script. It was an infinite loop that made the system full. I interrupted UBUNTU's own check disk. And tried the WINDOWS one!! I'm now reinstalling UBUNTU 12.1 and I have a semi recent version of the program I spent months writing and improving. The moral of the story - ALWAYS get the latest backup. Anybody with same problem should read http://en.wikipedia.org/wiki/Wubi_%28Ubuntu_installer%29 and http://ubuntu-with-wubi.blogspot.fr/2011/08/missing-rootdisk.html. May be you're lucky enough that your root.disk isa save in found.000.