Make sure you are using 5.2.12 version. All previous 5.2.x versions have security issues. Since someone is able to modify your index file, you are not secured. It seems that your website/server has security issue. You will have to check the logs (ftp, web server etc.) for the time when the file was modified.
Better to install whole *updated whmcs again and restore backup.First create backup or i think you're getting database backup in your email .Restore the same which you think is clean and recently updated .
█ Fastest . Reliable . Affordable Web Hosting by MNCHOST.COM
Your server has been compromised either by using exploit on an older whmcs version, or ANY OTHER outdated software/CMS on your server.
First, clean up your hosting server and remove any malitious software/malware.
Install a FRESH copy of the LASTEST whmcs - 5.2.12. Don't reuse older things such as custom scripts, templates, etc. If you really need to use something from your old whmcs installation - CHECK IT MANUALLY to ensure it's not being exploited.
As other suggested, your entire installation is compromised. I suggest you do a fresh installation. Also, if it is possible, setup it on another server. There is a possibility that your entire server is vulnerable.
Can't believe I'm reading this 5.2.0? Yikes man that came out on the 1st February 2013. So outdated, I suggest you do what the above have said ASAP, and then keep a eye on your emails (from Whmcs), WHT forums here: http://www.webhostingtalk.com/forumdisplay.php?f=233 (New forum, outside that is the old ones)
haha is it a nulled software.. If you want to be serious about hosting, you can't use freeware or nulled softwares
█ CheapWindows VPS | Linux VPS | Dedicated Servers Within Your budget
█ Accept Credit Cards, PayPal, Payza, PerfectMoney, Moneybookers, BitCoin and ....
█ Instant Windows and Linux VPS Activation