Operating on IndesignCC.
Each document in the book has the swatch called “chapter key colour” (or whatever) and this is used for paragraph, character, table, cell and object styles. Then we change the values for that swatch in each individual document so that each document has it’s own chapter colour. This works fine until we need to synchronise the styles across the book, eg we might need to change the spacing on a heading style or maybe move something on a master page or something else. We ensure that “swatches” is NOT ticked in the list of things to synch, then we synchronise and InDesign updates across the book but also synchronises the swatches which we have specifically unticked, resetting the chapter key colour swatch to whatever it is in the reference document. We then have to go back to every document and redefine the values for the chapter swatch.
As you have seen in this other thread, it seems that swatches always sync, even if you tell them not to. It should do what you tell it to do, so in my opinion, this feature isn't working properly. Your only solution at this point seems to be to use a different name for the swatch in each document. Maybe call them Chapter Key Colour 1 and Chapter Key Colour 2, etc.
If you wish to contact Adobe directly on this, you may report this at the following web page: https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform&product=12
Here's what I wrote in a bug report that I just posted:
Concise problem statement: Synchronize book will synchronize swatches even if Swatches is deselected in the Synchronize Options.
Steps to reproduce bug:
1. Make 2 documents
2. Make a book
3. Bring the 2 documents into the book
4. Create a new swatch in Chapter 1 called A
5. Create a new swatch in Chapter 2 with the same name as the swatch in Chapter 2, but with different values
6. Go to the Synchronize Options and deselect Swatches from the Styles and Swatches list
7. Synchronize Chapter 2
Results: The swatch values of the swatch in Chapter 2 will change to the values of the same-named swatch in Chapter 1
Expected results: Because Swatches was set to not synchronize, the swatch in Chapter 2 should have retained it's values
EDIT: I made a typing error in step 5. It should have read:
5. Create a new swatch in Chapter 2 with the same name as the swatch in Chapter 1, but with different values