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I have 301 redirects which direct /index.html to /site folder and when I created a subdomain it also redirects the link to /site which causes 404 Not Found.

For example: members.mysite.com redirects to members.mysite/site which causes 404 error can I add execption for specific forlder or something without changing the redirect.

.htaccess content:

AddType text/x-server-parsed-html .htm .html
RedirectMatch 301  ^/index.html(.*)$ /site$1
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.htaccess rules apply to every subfolder that are within the folder with that .htaccess file. To stop your root .htaccess file affecting your subdomains, you should create your subdomain folders outside of the public_html folder on your server.

Also the problem with your redirect is that you are using redirect match, try a redirect that specifies the absolute path, such as:

RewriteCond %{HTTP_HOST}  ^www\.mysite\.com$ [NC]
RewriteCond %{QUERY_STRING}  ^$
RewriteRule ^index\.html$ /site? [R=301,NE,NC,L]
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