Did you check (for example with FTP) if this PDF-file still exists in the folder assets/uploads/?
Not sure what you exactly mean by that.
With the default .htaccess file
...
# The Friendly URLs part
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
MODX only runs (RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]) if the requested file doesn’t exist on the disk (RewriteCond %{REQUEST_FILENAME} !-f).
When the 403 forbidden message is displayed, it doesn’t seem that MODX runs at all.