Hi Emily
If you do a theme update you will not lose any of the settings you have put in the Tempera Settings area. If you want to be doubly safe you can always do a quick export of the theme option anyway as a backup, and then re-import them if needed (see this on the right side of the Tempera settings screen). As long as any custom CSS is in the appropriate miscellaneous area too you will not lose that.
I hope this helps
Jim..