Index.php is recreated automatically

If you see a folder or files recreated automatically that means that you are being attacked.
The hacker found a vulnerability in your PHP version and pushed the following command to your server 

That will cause a lot of problems for your site.
You will have code injection and probably the website will become extremely slow.

Before you start investigating and cleaning the infected site do the following first to prevent the malicious code to run in server memory.
Go to Service SSH --> Process list and stop the one that looks like the one above

Then you will be able to work with peace of mind.

Next, upgrade your PHP versions.

If you had your site filled with hacked .htaccess files run the following command to clean all of them instead of browsing each folder

Hope those tips will save you the day. If not get in touch . I will do the job for you!