Domain Mapping resulting in https permalink structure

So my organization has 2 Multisite networks; sites.orgname.edu and departments.orgname.edu. Currently we have 2 sites that need their own domains. 1 site is currently in the sites network, the other is in the departments network. When we change the sites domains, everything works okay, however, the permalink structure defaults to https. The site can be viewed at http, however the permalink structure is https and adding media uses https url and viewing pages defaults to https. How does this happen? How do I fix this? The sites inside the current networks (sites, departments) work like normal. Why is it only when I change to new domains?