Hi @sathya66 ,
in my humble opinion you should have a checklist of every customized file you have, as those are the ones that are prune to come back to SDW configured defaults after a hotfix or maintenance is applied in your system.
This best practice is not only true for the technical customization (such as server.xml, sasv9.conf, etc), but also to many functional/business customization. Some examples could be: themes, solution domains, etc etc.
I would suggest you to start creating such checklist document, it will help you a lot!
Best regards,
Juan