My WordPress website auto updated and therefore now Visual Composer no longer works. I have edited my theme and I am worried my changes may be lost if I upload the new Fortuna theme.

IS there anything i can do to make sure my changes aren’t lost.

What part of the theme you updated? That’s why it’s a good idea to use a child theme if you are to do some mods, read more here:

http://blueowlcreative.com/docs/fortuna/#customization1

What you can do now is simply compare the files (use Winmerge for example) to track down the code changes you have made to the main theme files (you can compare the original theme files from the version you have isntalled and compare with your current). Then once you install the new theme version, install a Child theme on top of it and add your changes to the child theme.
Good luck!