You tried to change a Modern site's theme from Change the look feature on Modern pages, but the theme is not reflected on the site.
To apply your Theme builder customization, ShortPoint inserts a Style-sheet in Modern sites. This Style-sheet will use your configuration to override the default SharePoint styles.
If you would like to apply colors via Microsoft's change the look feature, you have to reset your modern theme builder's customization. This would remove all ShortPoint customization from the site.
Follow these steps to reset the theme builder
1. Go to ShortPoint's dashboard
2. Click on the Theme Builder tile
3. Under Modern theme, click Reset to original site settings (modern)
That's all, changing Themes from modern change the look should now work as expected.