You should never (almost) modify free/premium themes directly. Beeing able to update themes is crucial for security and compatibility reasons.
If you make any changes to the theme directly, then all these changes will get lost after update and you'll have to make them again and again.
On the other hand WordPress allows you to create Child Themes and that is the recommended way of modifying other themes.
So if your changes are lost after update, then you should:
- Get backup of your previous, modified theme.
- Get all your changes from that theme.
- Create your child theme and use it to make your changes based on new version of that theme.