It looks like if both communities are on the same domain then users can move inbetween then. In this case, I have added my community to the same domain and changed the path so they are still different. This got me around the issue.
It seems like what you're looking for is SSO with salesforce as both the SP and IP. I've never tried it within the same org however. Here is some info that you can try to use:
Salesforce to Salesforce SSO
SSO in communities
In theory, you set up SSO, Then you enable your community to use SSO pointing to Salesforce as the IP, then you create a login flow ...