Hemant Vishwakarma: SilverStripe 3: Can no longer access CMS admin area, receiving 500 error

When trying to access the CMS via /admin on a live SilverStripe site it's suddenly starting producing a 500 error page with the following message the rest of the site is fine:

The server encountered an internal error or misconfiguration and was unable to complete your request.

The most recent errors in the error log in the public_html folder shows:

[17-Nov-2018 03:06:11 UTC] PHP Warning: Director::protocolAndHost() lacks sufficient information - HTTP_HOST not set. in /home/mysite/public_html/framework/control/Director.php on line 488

The error log in cPanel shows:

[Wed Nov 21 15:27:24.578366 2018] [core:alert] [pid 10504:tid 47515481941760] [client 90.242.226.###:56737] /home/bwib/public_html/.htaccess: Invalid command 'SetEnv', perhaps misspelled or defined by a module not included in the server configuration

I've checked the .htaccess file and its somehow changed to this:

# BEGIN cPanel-generated php ini directives, do not edit
# Manual editing of this file may result in unexpected behavior.
# To make changes to this file, use the cPanel MultiPHP INI Editor    (Home >> Software >> MultiPHP INI Editor)
# For more information, read our documentation (https://go.cpanel.net/EA4ModifyINI)
<IfModule php5_module>
    php_value date.timezone "UTC"
</IfModule>
# END cPanel-generated php ini directives, do not edit

If I replace it with the original .htaccess file the entire site breaks and I get a 500 error.

Original .htaccess here:

### SILVERSTRIPE START ###
# Deny access to templates (but allow from localhost)
<Files *.ss>
Order deny,allow
Deny from all
Allow from 127.0.0.1
</Files>

# Deny access to IIS configuration
<Files web.config>
Order deny,allow
Deny from all
</Files>

# Deny access to YAML configuration files which might include                                 sensitive information
<Files *.yml>
Order allow,deny
Deny from all
</Files>

# Route errors to static pages automatically generated by SilverStripe
ErrorDocument 404 /assets/error-404.html
ErrorDocument 500 /assets/error-500.html

<IfModule mod_rewrite.c>

# Turn off index.php handling requests to the homepage fixes issue in apache >=2.4
<IfModule mod_dir.c>
    DirectoryIndex disabled
</IfModule>

SetEnv HTTP_MOD_REWRITE On
RewriteEngine On
RewriteBase '/'



# Deny access to potentially sensitive files and folders
RewriteRule ^vendor(/|$) - [F,L,NC]
RewriteRule silverstripe-cache(/|$) - [F,L,NC]
RewriteRule composer\.(json|lock) - [F,L,NC]

# Process through SilverStripe if no file with the requested name exists.
# Pass through the original path as a query parameter, and retain the existing parameters.
RewriteCond %{REQUEST_URI} ^(.*)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule .* framework/main.php?url=%1 [QSA]