I've found some malware (some javasrcript from campaign ID) on a wordpress site that I set up. I'm going to reinstall wordpress to remove it, but am wondering if the atahualpa theme, and all the customizations I have done to it, will be deleted when I reinstall wordpress. I do have daily backups to the database.
Thank you.

The options are stored in the db, unless you have changed the theme code. If you were hacked, I would refresh every theme and plugin you have.

Ok. Thanks. I made no changes to the theme code, just many setting adjustments and some css inserts.