Hello, at this time when you sync a map area it is just syncing operational layers (ie uploading changes to editable feature layers and downloading changes from feature layers). The properties of the map itself, like bookmarks, are not updated. Right now to get these changes on the mobile device you would need to redownload the map area.
This is a feature we have looked at adding, but it is not currently planned for a release. You could add an Idea or comments to an existing one like - Update complete webmap including form definitions during regular sync (and not only the data) to help us better understand what behavior you would expect (like would you expect/want other map properties to "sync" as well).
