My redhat 5.5 server was running fine. Next day I have come to know server is not running. Upon checking I have come to know that OS files are no longer there like /etc/inittab, /etc/fstab etc....
First How to investigate what was happend....
Secondly How to recover Or rebuild the system....

Do you have a backup you can restore from?

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first advice: switch it off, don't use the hard drive, unhook it from the network, investigate from a separate OS (e.g. Live USB).

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You seem to be running an out of date version of RHEL, however this is not meant to indicate this was the problem. The problem appears to be something much more serious.

Hopefully you have a backup, as hydrurga suggested.

Also as ondoho suggested, you should investigate using a live boot media.

I'm curious however to find out how you know the specifics about the files which are no longer there, and also the other circumstances surrounding this. Such as:

1. Does anyone else have access to this server that you know of?
2. How exactly did you make this determination about these files?
3. You've cited /etc tree files, is this the only tree affected?
4. When you say it was not running, what specifically do you mean? Off? Not responding? Console Y/N? Accessible from network Y/N?

As far as how to rebuild the system, I suspect you can do a complete fresh install, hopefully relying on the possibility of a backup to return it to the former good state. Unsure how much you can benefit if you happen to have support from RedHat versus not, that version is on extended support though. The questions there are whether or not you have release disks or media to perform the re-install and rebuild of your server, or if you should upgrade to a newer version.