I checked Endnote’s bibliography sort order for the Chicago 16th Author-Date output style file and ran a test which shows the bibliography is sorting the Year field in ascending order (oldest to newest). To reverse order the bibliography would be incorrect for Chicago 16th style guidelines.
The citation separator could be changed from a comma to a semicolon but that doesn’t appear to conform to the Chicago 16th style. If you wish to persist in changing the citation separator, which may be incorrect, the citation separator can be changed in the Citation “Template” of the output style file.