The only thing to do is to check. Security experts say that such a system is no longer trusted. The employees have to reestablish trust in the data and also in the programs. Criminal hackers have been known to insert their own changes to certain computer programs. Criminal hackers often leave what are called back doors into the systems they've already broken into.
Back doors allow the hackers to re-enter the compromised computer systems anytime they want.
This kind of change to system software is a real threat to the people that have been victimized. It can take days to check all of the information on a computer system that has been broken into. Sometimes the checking costs hundreds of thousands of dollars in wasted salary or consulting fees. I remember that when I was in charge of a big computer center in the 1980, my staff and I would spend from midnight to 6 in the morning every day for five days testing the new version of the computer operating system that the computer maker had sent to us. Now think about why on earth we would trust a production system that might have been damaged by a criminal hacker.