I'm not sure if your requirements to use #flux are already set, but over some time "Redux turned out to be the better Flux". If you haven't started yet, have a look on Redux.
Regarding Stores, they have a clear statement here:
It’s important to note that you’ll only have a single store in a Redux
application. When you want to split your data handling logic, you’ll
use reducer composition instead of many stores.
So they have a good receipe to solve a problem you might be facing right now when doing classic Flux.
But also, sorry for not answering your question ;)