Any clue on how i can tell it to automatically change all new/modified files?
No. Well, not how to do it `the GNU/Linux' way (by use of some file alteration monitor).
But, I have another idea:
1) ssh/telnet onto the linux box
2) mount the windows disk/share/...
2) cd into backup dir
3) run a makefile which copies all the data that should be backed up.
You could of course create a new user (`backup_script_01') which logs into a shell script that does that; then all you have to do is ssh.