What potential issue could be causing every 2nd line in the PHP code to become empty when uploaded to the web server?

The issue could be related to line endings. Windows systems use CRLF (Carriage Return Line Feed) while Unix-based systems use LF (Line Feed) only. This can cause every 2nd line to appear empty when uploaded to a Unix-based web server. To solve this issue, you can convert the line endings to Unix format using a tool like dos2unix or by configuring your text editor to save files with Unix line endings.

// Convert line endings to Unix format
$content = file_get_contents('file.php');
$content = str_replace("\r\n", "\n", $content);
file_put_contents('file.php', $content);