I assume that what I am asking about is being saved in the post meta. Advanced Custom Fields data is preserved when merging back into the page but if I allow them to have those fields on the alternate post custom post type they don't see the original data and can overwrite the custom field info without having the original to work from.
Also we were using User Access Manager which seemed to be working great. The group assignment is done in a meta box in the page. When editing the alternate version the group is checked but upon merging back into the original that value is lost and the access is wide open again.
I've tried your section groups but it isn't exactly what we are looking for. UAM hides all pages except the ones that are assigned to the group thus only allowing them to clone those pages.
Any help with this is greatly appreciated.