Hi @Abdulazeez Asaju ,
Thank you so much for coming back and sharing the solution.
Since this may help others who run into the same behavior, so I would like to make a short summary of the issue.
Issue:
applicationHost.config and redirection.config kept disappearing from the IIS config folder. They could be restored in Safe Mode but were gone again after a normal boot. The cause was a malicious driver that loaded during a normal Windows startup and was hiding or removing them.
Solution:
Windows Defender detected the threat, but it kept returning when removed during a normal boot. OP traced the driver in Safe Mode and disabled it there, and after restarting normally, applicationHost.config and redirection.config stayed in place and IIS worked again.
One thing worth keeping in mind is that disabling a driver stops it from loading but leaves it on the system. Since it was there before the server was purchased and survived a reinstall, the base image is the likely source, so a clean image from the provider would be the safer long-term fix.
If you find this answer helpful, I would greatly appreciate it if you could follow the instructions here so others with the same problem can benefit as well. Thank you.