The option “Remove files not on source” is available for one-way syncs in the Destination tab in the sync settings. If enabled, all files and directories that are not on the source (anymore) and are not explicitly excluded will be removed (see Filters). This option is always enabled for two-way syncs.
The option “Remove excluded files”, which you can find in the Advanced tab in the sync settings, removes all files that are excluded by any of the filters in the Filters tab. As an example, this option can be useful to remove hidden files left over by a previous copy performed in the Finder. In this case it is recommended to enable this option only at the beginning, run the sync once, and then keep it disabled, so that it will leave hidden files such as
.DS_Store files (which store Finder metadata) and the
.Spotlight-V100 directory (which contains the Spotlight index) alone.