The Swatches panel in Adobe Illustrator is a frequently visited, yet somewhat misunderstood tool.
First of all, it's the one place you can quickly see what colors are being used in your document. But that's only if you choose 'Select All Unused Colors' from the panels option menu. Then choose 'Delete Swatches' from the same options menu. This is something you should frequently do so you can keep focused on your color usage in your document.
A frequently mistaken notion about the Swatches panel is that the colors in the panel are all in the document. Whereas it is a good idea to delete unused swatches for organizational reasons, it is not essential to the functionality or printability of the document. It's the difference between the word 'has' and the word 'uses'. Look at it as an artists canvas and paint palette. Just because an artist has thirty separate dollops of color on their palette doesn't mean they've used those thirty colors on their canvas. If somebody proofs your file and tells you you've made an error by having too many swatches in the file - just nicely point out to them that it is not an error and why, but then clean up the swatches just for the sake of it.
Where it may cause errors is if you use too many spot colors. But more often than not you will get a message when trying to print to a home or office printer that your document uses too many spot colors. Keep in mind your final printing method and pare down colors accordingly. If the job is going to be printed professionally on a litho or similar press, find out from the print vendor what their maximum press colors are and adjust your file accordingly. It's usually six to eight colors. If it is strictly a CMYK job, you can have a multitude of swatches. Just make sure they are set as process colors instead of spot colors.
One annoying thing the Swatches palette does in Illustrator is the reappearance of deleted swatches. On occasion they'll just pop back into the palette after you've gotten rid of them. Not sure why this happens, but again it's not a error that will lead to the dysfunction of the file.
There are also useful, yet sometimes, problematic issues that happen between Illustrator and Photoshop and their shared color palettes. But more on that in a future posting.
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