How can you protect your software on the computer?

The best way is to do an 'image' (a kind of snapshot) of your disk drive and save it to a different drive. There are many software tools to do that... one which works well for Windows and is free is BootitNG. When you need, or go through a disaster, you can override the disk drive with its older image and restore it to what it contained then. This is foolproof compared to Windows System Restore (I do not know much about its Apple equivalent Time Machine so I cannot comment.

Imaging software has been developed for rapid deployment of systems on numerous machines.