I think your problem lies in that you are directly fetching a file that is stored on the server, as opposed to using PHP to "serve" this file programatically. This isn't the first problem you will encounter with this method, you also can't check for security or get the file from external file storage (generally speaking, you don't store files directly on the web server these days!).
But, simple to do once you know how :)
Firstly, lets change the URL you download your file from to something like https://example.com/download.php?token=A6FZ523
So, we are sending a GET variable to a php script named "download.php". In that script you will have something like the following:
<?php
$token = $_GET['token'];
// Get the information about the file from the DB, something like:
// SELECT filename, size, path FROM files WHERE token = $token;
// Giving you $filename, $size and $path
header('Content-Description: File Transfer');
header('Content-Type: application/octet-stream');
header('Content-Disposition: attachment; filename=' . $filename);
header('Content-Transfer-Encoding: binary');
header('Connection: Keep-Alive');
header('Expires: 0');
header('Cache-Control: must-revalidate, post-check=0, pre-check=0');
header('Pragma: public');
header('Content-Length: ' . $size);
echo file_get_contents($path);
// This will be on a completed download
// INSERT INTO downloads(date, tokenID) VALUES(CURRENT_TIMESTAMP, $token);
?>
When the download.php file is called, the token is taken and matched to a file's info in the DB. You then set headers which basically tells the browser "this is a file", your browser responds accordingly by implementing a file download as normal. You then read the contents of the file to the user. Once this has been completed, you can log the download via another DB call.
A big thing to say is that this script (obviously with the DB calls written in) should do the very basics for you, but there is a lot more to add depending on your usage scenario. Think security, input validation, where you store your files and sending a MIME type header.
Hopefully that should point you in the right direction though :)