Is the course content in the database?
I also don't understand why missing icons would break the front page layout. And, I am only talking about the front page. The other pages are ok. Probably because they don't access the courses.
I image that "All Courses" page is probably affected but I didn't check it at the time it was broken.
The links are NOT in the code as I completely removed the old theme and we have not customized any other part of moodle.