Sales : Logo of Salesforce Classic Apps Not Visible in Lightning Experience

To resolve this issue, upgrade the app to a Lightning app and re-upload the logo.

Steps

1. Navigate to Setup → App Manager
2. Click the dropdown arrow (▼) next to the target app and select Upgrade
3. Enter the App Name and Developer Name, then click Upgrade
4. An error message ("An error occurred while updating the record") may appear, but the Lightning app is still created
5. Click the dropdown arrow (▼) for the upgraded app and select Edit
6. Upload the logo under App Branding and click Save

Additional Information

Logos configured for Salesforce Classic applications may be replaced by default images when viewed in Lightning Experience because branding settings are not carried over during the transition.