WHM Not Listing Account, DNS Etc, Missing Files, File System

I recently had an issue where my box wasnt listing accounts (on logging into WHM for the first time it would, thereafter browsing different functions in WHM it would fail to list any accounts), would not list any zone items when editing DNS zones and in general was acting very strange.

I think the tech support chap narrowed it down to zero free inodes on the filesystem (i was even getting errors when editing files with 'vi'). This was increased for the VPS and all issues seemed to be resolved...

However named and httpd were not starting after reboots. Again on looking closely named and httpd were missing from /etc/init.d (on CentOS 5.3)! This is very strange and i certainly didnt modify those nor delete such critical files.

For a second opinion, is there any cPanel script that can be ran to fix the issues, i am concerned other things have been affected but havent manifested themselves yet (other files deleted etc). Does cPanel update script create the init.d files or is this done by the CentOS operating systems itself? Are these files modified during a cPanel update script?

These init.d files for named and httpd have been readded (copied across from another box) and it seems to be ok again, but ideas on howto proceed much appreciated, as i mentioned i dont want any nasty supprises!