Sometimes I’ve seen some problems when the instance of Dynamics updated to the Dynamics 365 and the Settings group doesn’t show all the options available, at least I’ve seen when was an update.
If this happens you can check if the option Show Group in the Settings area is checked. You can do this by using the XrmToolBox application, with the SiteMap Editor plug-in, or you can download a solution that contains the Sitemap and check if that property is in the Settings area.
Then you just need to upload your Sitemap and the groups will show up again.
Hope this helps.