A related report:
Select Unused Swatches does not select the second black swatch in Grays color group
http://illustrator.uservoice.com/forums/601447/suggestions/49256807

This behaviour truly is a big problem and burned us at work many times!

The command "Select All Unused" should NOT select global colors that are in use inside symbols. I really hope Adobe will fix this soon.

See also this forum post:
https://community.adobe.com/t5/illustrator-discussions/colors-considered-as-unused-in-symbols/m-p/14272190#M389588
Symbols should remember what colors they use and not convert them to black and named "Deleted Global Color"

Hi all,
After my question on the community and following a suggestion from Laura Coyle, I post my request.

I turn visuals (most of them with Pantone color ref) that are provided to me into symbols to take advantage of the flexibility and security they offer.

I've just realized that when I turn a visual into a symbol (without keeping the visual in its original form) and ask to select the unused colors (in the color palette), the constituent colors of the symbol are considered unused.

In order to lighten my many files, I run a script that eliminates what is not used (including nuances) so I end up with files with visuals without color information.

As the symbols are actually in use on the artboard, it should include those in "used" colors

Thanks in advance

I made a post about this as well, but I just upvoted this one.

Just got burned again by this issue. We place some of our spot color cut paths inside symbols, and when we clean up our files sometimes that color gets deleted.

Then when it goes to our rip the cut path isn't seen correctly and is not turned into a cut path, instead it actually prints and ruins the artwork.

This should really be fixed. Illustrator should know when colors are in use, regardless of if they are on the actual artboard or not.

The problem is:
If you "Select Unused Colors" and delete them, color swatches that are used inside of Symbols are deleted if they're not used elsewhere in the artwork outside of the Symbol. Behind the scenes, those colors are apparently assigned names numerically like “Deleted Global Color 5”. These names are revealed if you choose to Add Selected Colors to the Swatch palette, or Add Used Colors.

This is bad enough because an element’s official Pantone colors are lost when one tries to tidy up the swatch palette associated with a document. Visually nothing changes in the document, but when we send to to manufacturing, the precise official color designations are lost and we have to re-do a lot of work.

It is DISASTEROUS when copying several such items into a new document. Completely different elements from Symbols used within different documents commonly will share the same basic “Deleted Global Color” name and instead of adding new swatches for different colors, Illustrator merges all subsequent instances of “Deleted Global Color 5” (for example) with whatever the first instance of “Deleted Global Color 5” is. This radically alters the appearance of artwork within symbols and is frankly, unacceptable behavior.

The correct behavior should be:

• Colors used in symbols should not be deleted when the user “Selects Unused Colors” in the swatch palette. The colors are in use after all!

• If that is for some reason unfeasible or turns out to be an undesirable behavior for the majority of users, then deleted colors should be assigned unique identifiers instead of the current behavior where radically different colors from different documents share the same default names.

We have tried to modify our workflow to stop encountering this problem, but keeping the swatch list tidy is important to streamlining our workflow. In a busy production environment, symbols can be sanity-saving, but when combined with good document hygiene, they become a nightmare all over again.