In InDesign 19.5.:
"Swatches synchronize when object, paragraph, or character styles are selected in the Synchronize Options dialog."

However, working with a book document with different color shemes in each chapter, this is a huge inconvinience for me.
I want to be able to sync my settings without syncing the colors, as they are deliberatly different in each chapter.
This change would cause the need to make a character/paragraph/object style for each chapter, causing the number of styles to be hard to manage.
Otherwise, I would have to change the colors after every sync or won't be able to use the synchronization anymore.

It sounds like a good idea to sync the swatches, but please make it optional.