There is no such thing under cPanel as an index.php page, so it wouldn't be overwritten.
You are going to have index.html placed back onto the account if it has been moved. I suggest either putting the content into index.html or adding a /scripts/posteasyapache script to move index.html and recreate index.php when it gets recreated on EasyApache recompile:
Code:
#!/bin/bash
mv /usr/local/apache/htdocs/index.html /root/index.html.`date +%Y-%m%d-%H%Mh%S`
cp /root/index.php /usr/local/apache/htdocs/
You'll likely need to "chmod +x /scripts/posteasyapache" for this to execute. You'll also need to place a copy of index.php into /root location for it to be copied to /usr/local/apache/htdocs folder.