If I have to do this project again, I will plan a version management system and instruct the team members to strictly follow it and verify the version of the files before uploading them to the live server.
First and foremost, always have up to date reliable anti-virus software with an Internet Firewall installed in the system. It is not possible to eliminate all threats as hackers and malware programmers cannot be eliminated. So the best policy is to prevent such attempts. In case a threat is encountered, the user has to report the issue to the anti-virus software provider, so that the provider can issue a fix for that threat as well. The system administrators can have security certificates and encryptions included in their web applications so that it is impossible for anybody to include viral software in the web application and spread it across the web.
As far as a backup system is considered, reliability is far more important than the features included. The main reason for using a backup system is to restore the original system if it encounters a sudden threat or gets corrupted. The backup system has to be reliable and error free so that it can actually serve its purpose. Limited features are sufficient for a backup system, as they do not play major role. In order to provide uninterrupted service to the end users, it is always essential that the backup system is reliable and is always ready to be used as a substitute.
In this case, resolving the problem depends on the nature of the issue and at times, even on the level of technical knowledge of the user. In any case, the basic things to check in the event of a complaint are:
The first thing to do is to stop continuing the changes try and reverse the changes done recently. It is best practice to take a screen shot or record the steps that are being taken. The database has to be checked to verify if the