The issue of a damaged ZIP file during WordPress export, caused by extra empty lines after the ?> closing PHP tag in theme files, arises because PHP's closing tag can inadvertently output whitespace or blank lines. Here's a breakdown of why this happens and how to fix it:

Why Does This Happen?
Output Issues: When a PHP script ends with ?>, any whitespace or new lines following it will be sent to the browser/output. This can corrupt the format of exported data (such as JSON or XML used in WordPress exports).
WordPress Exporter: The WordPress export process heavily relies on properly structured XML. Any unexpected whitespace or characters can corrupt the resulting file, rendering it unreadable or "damaged."
Best Practices to Avoid This Issue
Omit the PHP Closing Tag: In PHP files that contain purely PHP code (no mixed HTML), do not include the ?> closing tag. This is a widely accepted practice to prevent accidental output of whitespace or other characters.
php
Copy code
// Your PHP code here

// No closing PHP tag needed
Check for Trailing Whitespaces: If you do include the ?> closing tag, ensure there are no extra lines, spaces, or characters after it. This can be verified by:
Manually checking the end of your files.
Using an IDE or text editor that highlights trailing spaces or blank lines.
Automated Tools:
Use linters like PHP CodeSniffer with WordPress coding standards to identify unnecessary closing tags and trailing whitespaces.
Configure your IDE or text editor (like VS Code, PHPStorm) to automatically trim trailing whitespace on save.
Fix for Damaged Export Files
If you already have a damaged ZIP file:

Correct the issue in your theme files by removing trailing whitespaces or closing tags where applicable.
Re-run the export process in WordPress.
Example
Bad practice:

// Some PHP code
?>

Good practice:

// Some PHP code

By following these practices, you can prevent issues with WordPress export files and ensure compatibility with various tools and processes.