When you delete a swatch that has been applied to an object in the document, InDesign prompts you for a replacement swatch. You can designate an existing or unnamed swatch. If you delete a swatch used as the basis of a tint or mixed ink, you will be prompted to choose a replacement.
Choose Delete Swatch in the Swatches panel menu.
Click the Delete icon at the bottom of the Swatches panel.
To replace all instances of the swatch with another swatch, click Defined Swatch, and choose a swatch in the menu.
To replace all instances of the swatch with an equivalent unnamed color, click Unnamed Swatch.