In place of seldom-used colour swatches, from v9.5.2 outlines instead draw the first (only) element from $Flags to the right of the outline icon of notes that are not selected and have a value for $Flags.
When a note with flags is selected, the flag is replaced by the link widget.
The syntax for setting flags, and the styles available are described in detail under their use as note flags in map view.
See also—notes linking to here: