ColorSwap by Jeroen Krielaars is a great After Effects plugin that helps search and replace colors broadly and subtly in the whole project while having an easy-to-use interface.

Jeroen Krielaars – ColorSwap Plugin Features

• Effortless substituting of colors: Search and effectively replace colors in selections, compositions, or projects in a heartbeat.
• Effortless color shifting: Make two project colors interchangeable with ease.
• Support for keyframes: Color changes over time are ideally taken care of.
• Search Scope: For effective color search, there are no constraints on the area you plan to search for.
• Ease of use: A mini UI is added, which brings optimal workspace management opportunities.

Aescripts – ColorSwap Documentation

Image 1: Switch between regular and mini UI to save precious screen space

Image 2: Easily search and replace colors within your comp

Image 3: Effortlessly swap colors across your composition, giving you full control over every hue in your design.

Image 4: Quickly replace color ranges and fine-tune the look of your animation with minimal effort.