Hi Pothi,
The server has a firewall and the site is scanned for malware regularly using the Securi service. The .htaccess file has always had 644 permissions and no other files have been affected.
I did install the Bulletproof Security plugin and then removed it as I thought it was responsible for the issue. I believe it may be some WP process that is updating .htaccess but don’t know how to identify it.