The Scheduler Site Profiles in version 15 were actually the local Site Profiles - there was no separate store of Site Profiles for Scheduler, it just used the site profiles of the user who installed the software. FTP Voyager 16 improves on this by setting up a separate Site Profile list for Scheduler, making it more easy to work with (especially for multiple administrators). If you do an in-place upgrade of version 15 to version 16 it should pull in the Site Profiles for Scheduler. If it does not, then you can easily address this by choosing the Site Profiles that were once in use in Scheduler from the "Browser | Site Profiles" menu (the local site profiles) and right clicking them, choosing "Copy to Scheduler" to copy the site profiles over and utilize them in Scheduler as well.
Hope this helps!