After reading/research documents in net, I setup my step-by-step Linux kernel up-gradation (Bash Script) in Debian. up-till now I upgraded more than 5 Debian kernels without any problem.
Read what to do here
And it's all done to avoid this problem:
I never found good documentation on upgrading/compiling linux kernel in Debian, Most of the time I stuck in between and my running libs gets corrupted, then same story; Put new hard disk, Install latest Debian, mount old HDD and copy all the contents.