In case of a failed or unsuccessful SP installation, the best way to correct this situation is a "Down Server Upgrade" as described in KB 3617668, performed with a DVD or CD's burned from a downloaded ISO, and also burned with no Anti-Virus active on the workstation.
Downloading and copying the Support Pack on a workstation and server without anti-virus software active is also the preferable option in general.
From this point on, this document describes an unsupported manner to verify the servers core OS files.
Before starting this procedure, make sure that there is a current and verified backup available.
Build a temporary server, which runs the same patch level of all products as the servers you want to compare, using a freshly controlled downloaded and burned Novell NetWare 6.5 overlay ISO of the Support Pack running in the servers.
If the original servers are running eDirectory 8.7.3.x on NetWare 6.5 Support Pack 7 or later and you want to build your compare server with the same version of DS, you first need to install a NetWare 6.5 Support Pack 6, then update that to the SP level of your production servers.
The core files of NetWare by default reside on C:\NWSERVER\ and SYS:\SYSTEM\
For being able to compare the files on the dos partition, execute these commands on the server:
set autorestart after abend = 0
After this, the C drive is mounted as a NCP volume named DOSFAT_C.
Use a file and directory compare tool of your choice and compare the contents of C:\NWSERVER and SYS:\SYSTEM\.
These Folders, Files and file-types MUST be ignored during the compare, as these are server or Volume specific:
.NCF files (especially STARTUP.NCF and AUTOEXEC.NCF)
NDS.* files and folders
SERVCFG.* files (these build up the server's registry)
The CertServ, NICI directory
Any files related to DirXML / IDM, as not all servers run this service.
These files and file-types may be ignored:
COREDUMP.IMG, or an other coredump image.
Backup files, as .BAK, .OLD, .SAV, ...
If you feel the need to compare the whole SYS volume, please ignore these files and folders in addition, as these are dependent on the products installed, or containing variables:
If during this compare of SYS a compare tool is used that can also access the _NETWARE directory, please ignore any differences of that directory as well.
If there is a need to verify the files for the additional services running on NetWare, please contact the Novell Support Center as several additional services have their specific files and directories.
Most commonly files not getting updated correctly is due to the fact that not all stoppable 3rd party services, like back-ups or antivirus scanners were halted or users were not disconnected which could cause files being in use.
Every now and then a Anti-Virus engine either during the handling of the Support Pack files on the Workstation, or the copying of the files toward the servers corrupted or deleted the files.
If the files that are incorrect are residing on the C:-Drive, the DOS partition, those files more than likely got a more recent date stamp than the ones of the Support Pack.