If they fall under FDA regulation, then they'll follow the same basic standards as everything else under FDA regulation. The FDA is not going to require flavoring manufacturers to give up their trade secrets or they would have done it long ago. This is why organizations like FEMA and the IFRA exist, so fragrance and flavoring industries can self-regulate and not give up their intellectual property. Little eliquid manufacturers mean nothing to the government. Giant flavoring manufacturers absolutely do mean something, and they will oppose this because even if it's not happening directly to them yet, it's an erosion of their rights to keep trade secrets protected.
Now banning flavoring in e-liquids like they banned it in tobacco products, that I could see happening but for the patently obvious fact that it wouldn't stop anyone from selling non-nicotine flavors for customers to mix themselves.