You would need to contact the author of your theme to update your theme to be compatible with the latest release of the platform.
If you use the filter on the theme templates page, you can filter for templates that have been modified. It will also tell you this on the upgrade warning. Note its not stopping you from upgrading, its simply warning you that they are modified and will be out of date when you upgrade, so you would need to update those manually.
There is a general guide on how to upgrade themes, which you can find in the following location, if you are doing this yourself