I had exactly same situation, I came to US with the visa of the first university. I thought it's waste of time to apply for another visa, as many suggested I could easily transfer the SEVIS and go to new university. But after I coming here International Students Office said, rules changed and it is clearly specified in I20 that I cannot transfer SEVIS unless I stay one semester. Luckily I had full scholarship in both the universities, only the second university was much reputed one. 

For me it didn't matter much, it was just a matter of university ranking. But in case you have to pay more as well. 

When I was in Kathmandu, I asked by email to US embassy, they said I should re-apply but I ignored and had to stuck with the original university. 

Here is my suggestion: re-apply for visa with new I20. You don't have to pay SEVIS, only visa application and visa fee i.e. 331 extra bucks. Even if they reject your new visa(highly unlikely, since you already have a visa), your existing visa won't be cancelled.

Good Luck!