.htaccess for Multisite keeps reverting to Single site .htaccess

Hello,
I’ve been having this issue and I hope someone can help me. I created a Multisite and have created a subsite. Now the .htaccess for my multisite is this:

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]

but when I try and access the site, somehow something changes my .htaccess back to this:

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]

I’ve tried making the changes and even changed the permission for .htaccess but to no success. What I did one time that work is take out the wordpress files in my folder and replaced it with a freshly downloaded one and that worked.

But checking again now it’s doing the same thing again. Any clues or ideas as to what causing this issue? Hopefully someone can point me in the right direction.

I’ve disabled the w3cache plugin so that hopefully it doesn’t interfere. I delete itheme security which also seems to cause other issues as well. Hope someone can help.

Thanks