2003 Toyota Camry Fried computer

Brought my car in to a toyota dealer for a check engine light problem, that I was told by an independent mechanic was a catalytic converter problem. He also told me that it should be covered by a government 8/80 warranty.
The problem is that when I went to pick up the car they told me that when they did a diagnostic on the car that they fried the computer. They told me it could take one to two weeks or as much as two months to fix my car. They gave me a loaner, but I'm concerned about what kind of problems I might have when I get my car back.