Try with this: remove the redirect part then use this insead:
RewriteCond %{THE_REQUEST} ^GET\ /apt/
RewriteCond %{HTTP_HOST} ^(www\.)?mysite.com$
RewriteRule ^apt/(.*) /$1 [L,R=301]
RewriteCond %{HTTP_HOST} ^(www\.)?mysite.com$
RewriteRule !^apt/ apt%{REQUEST_URI} [L]
then use the same code for the main website.