Howdy!
I’m from Automattic, the team behind Jetpack. I’m working with a mutual user with a large multisite using Cloner to clone sites.
When cloning a site with an active Jetpack connection, Cloner is also copying over the “unique” bits in the database that will cause issues for both sites and their relationship with WordPress.com.
Specifically, for both sites to operate as expected, we need to not clone the jetpack_private_options row in the options table. On the original site, it contains an array of the unique values for the site. The lack of one on the destination site will simply require the user to connect to Jetpack, leaving the rest of the settings as set from the cloned site.
Any suggestions on the best place I can suggest to the user to hook into would be appreciated. If possible, it would be great if this could be added as an integration as well.
Thanks!