The VA rep I talked to on the phone was clueless and said she'll find out and call me back . The veteran counselor at the school has no idea and told me to call the VA, so I'm stuck and don't know what to do.

Backstory, I applied and was accepted to Kennesaw State. Before I started or even submitted my GI Bill verification letter to KSU, I was notified that my program was dropped. So I applied to Chattahoochee Tech, got accepted and am supposed to start in June. When I applied for the GI Bill, I listed KSU as the school, but now I'm going to Chatt Tech instead.

Does it not matter and do I just submit the letter I already have?, or do I have to go back through the VA and reapply under the new school?

Doesn't matter what you put on the initial application.  Do you have a current letter from the VA that lists current/remaining months go GI Bill?  If so, that is all you need to take (a copy) to the VA rep at the new school.

Which GI Bill btw?  Got an eBenefits account?

Doesn't matter.  Take your NOBe to the veteran's rep at the new school's financial office/registrar.  They certify your enrollment and you gets your money