Hi Steven Lancaster,
1. Delete search indexes you have created from Sitefinity UI.
2. Go to App_Data/Search folder and from there delete the folder that has the same name as the problematic index
3. Go to the page where you have dropped SearchBox
control and remove it.
4. Go to the backend UI >> Administration >> Search and recreate the index. Then run it.
5. Return back the page were SearchBox control was, drop it again and set your index from "Select an index" DropDownList.
the Telerik team