The documentation for Azure Active Directory B2C states ADConnect can’t be used to migrate users. I believe this is referring to the native store.
“No, Azure AD Connect is not designed to work with Azure AD B2C.” https://docs.microsoft.com/en-us/azure/active-directory-b2c/active-directory-b2c-faqs
But can I use ADConnect if I configure Azure Active Directory as an Identity Provider?