how to edit a active prompt in customize navigation in console as error shown custom theme color value set to dark.

This sounds like the "Create Prompts" unit of the User Engagement module, where you build the targeted prompt "Get Help Anywhere in the Console App" in the Sales Console. In that unit the custom theme color is optional ("If you want to select a custom theme color..."), so if the challenge check complains about the theme being set to Dark, the simplest fix is to edit the prompt and remove the custom color (or switch it to Light), then check the challenge again. 

How to edit a prompt that is already active: 

1. In your Trailhead Playground, go to Setup, type "in-app" in Quick Find and open In-App Guidance. 

2. Find "Get Help Anywhere in the Console App" and from the row-level action menu choose Edit. The In-App Guidance Builder opens in a new tab. (If the builder opens on another app, use the App Launcher to open Sales Console.) 

3. In the builder bar, open the "On This Page" list and select the prompt, then click Edit. 

4. On the position/appearance step, uncheck "Use a custom color for in-app guidance" (or keep it and choose Light), click Next, and Save. 

5. Click Settings in the builder header if you also need to verify the action button URL, schedule (End Date about 3 months out, Show when the page loads, Times to Show 2, Days In Between 5), profile/permission options and the API Name GetHelpAnywhereintheConsoleApp. 

6. Click Done and run the challenge check again. 

If the Edit option is greyed out or the builder won't save, an alternative is to delete the prompt from the In-App Guidance page and recreate it following the unit steps without choosing a custom color. Also make sure the Trusted URL for

(API name help_salesforce_com, img-src enabled) exists, since the same challenge checks it. 

Unit:

Considerations for Creating In-App Guidance:

Assumption: your post doesn't include the exact error text or unit name, so I am assuming it is this unit and that the checker message refers to the prompt's custom theme. If it is a different unit, please paste the full error message and the unit link.