I have a strange issue with the file system, for some reasons there is one
directory that contains some files and I am able to see them using ndir or
attrib and event edit them but I could not see them in windows explorer or
using dir or event copy those files. Are there any special attributes get
added by Tivoli tsm or Netshield? And is there is way to remove them?

Here is the list of software running on server:

Netware 6.5 with SP3 and some post patches
Netshield v6.2 - received utility NLM to remove extended attributes put on
by Netshield but it did not fix the issue
Tivoli TSM v5.3.0
HP Secure Path
HP Nic teaming

Any suggestions