SSL on subdirectory multisite with Domain Mapping plugin

I have 9 subsites set up on my multisite, and I'm trying to get SSL working for each site. Each subsite is setup as a subdirectory, e.g. site.com/subsite, and mapped to a domain, e.g. subsite.com, using the Domain Mapping plugin. Before the subsites are mapped, SSL/https works. After the subsites are mapped, SSL/https does not work and I get a security warning in my browser. How do I make this work? Thanks!

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