you can always remove the link and recreate it or just cd linux-2.4.20 is also fine.

You can put the kernel tree wherever you like. The steps involved(at least that is what I do)

1. cd linux
2. make mrproper(clean up stuff)
3. cp /boot/config-2.4.20-xfs ./.config
4. patch -p1 -N < ../any patch files which I put at the parent directory
5. make menuconfig
6. make-dkpg kernel_image
7. cd ..;dpkg -i the_generated_kernel.deb