I have shops setup on subdomains in a Wordpress Network then mapped out to real domains with a plugin. Works fine.
In the factory settings I have to put subdomain.domain.com to be able to MANUALLY update my shops with products and settings. If I put in domain.com it does not work.
However the automatic updates do not work because of a domain mismatch error.
ERROR: factory_fatal (domain_mismatch) error:816,call.updater.read_update:714,update_from_path:3463,read_local_update:3439,do_remote_update:3417
It's about shops: 14966 and 14745
I will PM you the whole error message.