After trying many known things I eventually created a satisfiable solution — bootable system. Not knowing how to fix Grub I decided to downgrade Grub 2 to Grub 1 and the only way to do this is using rescue mode on Debian install disc. The procedure goes as follows:

• Boot from Debian install disc for architecture you use (i.e. amd64). In the boot menu choose help option as it offers you the option to use the “old-style” command line boot options. The default rescue-mode shell lacks some variables needed for installing/removing packages form the system, so it is useful to start rescue-mode with the following boot option (it enables the user input needed during some instal/remove processes): rescue debian-installer/framebuffer=false
  It is also possible to do this later by running TERM=vt100; export TERM in command-line.
• Follow the procedure that looks pretty much as installation procedure, but after certain point it offers you the option to choose the partition to use as a root system. At this point it is good if you know which one is it. Next menu lets you enter the command line in which you can alter your system.
• Using apt-get I first removed the Grub 2 installation (just in case leaving behind configuration files) and then installed the grub-legacy package. After some configuring
#grub
grub> find /boot/grub/stage1
(hd0,1)
(hd1,0)
grub>root (hd1,0)
grub>setup (hd1)
grub>quit

  and
  
#update-grub

  the new “good-old” Grub 1 installation was ready for reboot.

Luckily the solution is simple. All you need is a live CD distribution with which you boot into your computer and reinstall GRUB (probably also Lilo – I don’t know because I don’t use it). I use System Rescue CD. It works with other LiveCD as well, but System Rescue CD was made for exactly this (kind of) job. It is a command line distro.

First run grub:

#grub

grub>root (hd0,2)

In my case (hd0,2) means 0 for the first (and only) disc in my computer and 2 is the partition number where my grub configuration files are residing (2 means the third (3) partition!!).

grub>setup (hd0)

hd0 in this case also means the first disc in the computer.

grub>quit

Reboot computer and you will see your familiar grub boot prompt.