PHP file automatically deleted

The first question is: what on earth is in your PHP files that they are so big in the first place. A normal PHP file with regular code is typically no more than a few hundred KB in size, hence the 1 MB file size limit.

Some tools pack arbitrary data (like images or other data) into PHP files as well. This can be a good method to prevent them from being accidentally opened in browsers, at a quite steep cost to server performance.

If that’s the case for your file as well, the best way to deal with that is to cut the arbitrary data out of the PHP file and into a separate file with a different extension. The remaining PHP code could then be altered to read the data from the separate file.

If the data you cut out is sensitive, you could use .htaccess rule to restrict access to these files instead.