Subdirectory wp-admin 404 error

Hi there,

I have had to re-install Ubuntu on my server, so copied all the wordpress files (/var/www) and have now unzipped them all the to same place again.

The main site shows fine: https://54.241.13.224/, but not the subdirectory sites (https://54.241.13.224/formidableapps/) unless you visit from their domain (https://formidableapps.co.uk/)

I also can’t access the dashboard for the site (https://54.241.13.224/formidableapps/wp-admin/)

Links to other pages across all the sites also only work with the default permalink setting (https://54.241.13.224/?page_id=40), not with any others (https://formidableapps.co.uk/mymoney/).

Does anyone know where I could start looking?

wp-config.php has multi site enabled (as it was copied from the old setup) and my .htaccess is:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [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).*) $1 [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]
</IfModule>
# END WordPress

# Change PHP memory limit, time limit,
# max post size, and max upload file size
php_value memory_limit 256M
php_value max_execution_time 300
php_value upload_max_filesize 32M
php_value post_max_size 32M