Stuck Notification Badges in Sidebar for Deleted or Inaccessible Repositories

[godcong]

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Hello GitHub Support,

I am experiencing an issue with the notifications page. In the left sidebar, several repositories still show notification badges (unread counts), but when I click on these repositories, the main notification area is empty. Additionally, when I try to access the related issues or pull requests, I receive a 404 error.

These notification badges have remained for a long time and do not disappear, even after I try to mark all notifications as read or done. I have also tried clearing my browser cache and using different browsers, but the problem persists.

Could you please help me clear these stuck notifications or investigate why they cannot be removed from the sidebar?

Thank you!

Best regards,
godcong

[github-actions[bot]]

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[DmitrySadovnikov]

This is the UI bug. Use Github CLI:

gh api notifications\?all=true | jq -r 'map(select(.unread) | .id)[]' | xargs -L1 sh -c 'gh api -X PATCH notifications/threads/$0'

[lcdss]

This is the UI bug. Use Github CLI:

gh api notifications\?all=true | jq -r 'map(select(.unread) | .id)[]' | xargs -L1 sh -c 'gh api -X PATCH notifications/threads/$0'

Thanks! I was having this problem for months and this worked for me.

[godcong]

@DmitrySadovnikov

Thank you for your response.
Although it didn't solve the problem, it provided me with significant assistance and insight, pointing me in the right direction for a fix.
I've now written a script that resolves the issue.

The issue is now half-resolved—the tags are gone, but they still linger in my list.
These items neither appear in my Watchlist nor exist in any actual project path.
So, they stubbornly persist in the Repo list, and I'm completely stuck.

# Mark all unread GitHub notifications as read
param(
    [string]$LogPath = "mark-notifications-log.txt"
)

# Function to write log
function Write-Log {
    param([string]$Message)
    $timestamp = Get-Date -Format "yyyy-MM-dd HH:mm:ss"
    $logEntry = "[$timestamp] $Message"
    Add-Content -Path $LogPath -Value $logEntry
    Write-Host $logEntry
}

Write-Log "Starting GitHub notifications cleanup script"

# Handle spaces in path to GitHub CLI
$ghPath = "D:\Program Files\GitHub CLI\gh.exe"

# Check if gh.exe exists
if (!(Test-Path $ghPath)) {
    Write-Log "Error: GitHub CLI not found at $ghPath"
    exit 1
}

Write-Log "GitHub CLI found at $ghPath"

# Test if we can execute gh command
try {
    $versionOutput = & $ghPath --version
    Write-Log "GitHub CLI version info: $versionOutput"
    Write-Log "GitHub CLI found and working correctly"
} catch {
    Write-Log "Error: GitHub CLI cannot be executed properly. Error: $_"
    exit 1
}

# Try different API endpoints to cover all notifications
$endpoints = @(
    @{ name = "All Notifications"; url = "notifications?all=true" },
    @{ name = "Participating Notifications"; url = "notifications?participating=true" },
    @{ name = "Basic Notifications"; url = "notifications" }
)

foreach ($endpoint in $endpoints) {
    try {
        Write-Log "Fetching from endpoint: $($endpoint.name) ($($endpoint.url))"
        
        # Get notifications as JSON
        $notificationsJson = & $ghPath api $endpoint.url
        $notifications = $notificationsJson | ConvertFrom-Json
        
        Write-Log "Total notifications received from $($endpoint.name): $($notifications.Count)"
        
        # Filter for unread notifications
        $unreadNotifications = $notifications | Where-Object { $_.unread -eq $true }
        
        Write-Log "Found $($unreadNotifications.Count) unread notifications from $($endpoint.name)"
        
        if ($unreadNotifications.Count -gt 0) {
            Write-Log "Processing unread notifications from $($endpoint.name)"
            
            # Mark each as read
            $successCounter = 0
            $failureCounter = 0
            $counter = 0
            foreach ($notification in $unreadNotifications) {
                $counter++
                try {
                    $repoFullName = $notification.repository.full_name
                    Write-Log "Processing notification #$counter/$($unreadNotifications.Count) (ID: $($notification.id)) for repo: $repoFullName"
                    
                    & $ghPath api -X PATCH "notifications/threads/$($notification.id)" 2>$null
                    $successCounter++
                    Write-Log "Successfully marked notification $($notification.id) as read ($successCounter/$($unreadNotifications.Count))"
                } catch {
                    $failureCounter++
                    Write-Log "Failed to mark notification $($notification.id) as read. Error: $_"
                }
            }
            
            Write-Log "Finished processing $($endpoint.name). Successfully marked $successCounter notifications as read. Failed: $failureCounter."
        } else {
            Write-Log "No unread notifications found in $($endpoint.name)"
        }
    } catch {
        Write-Log "Error fetching from endpoint $($endpoint.name): $_"
    }
}

# Additionally, try to mark all notifications as read by repository
try {
    Write-Log "Attempting to mark all notifications as read by repository"
    
    # Get all repositories with notifications
    $allNotifications = & $ghPath api notifications?all=true | ConvertFrom-Json
    $repos = $allNotifications | Select-Object -ExpandProperty repository | Sort-Object -Property full_name -Unique
    
    Write-Log "Found $($repos.Count) repositories with notifications"
    
    foreach ($repo in $repos) {
        try {
            $repoName = $repo.full_name
            Write-Log "Marking all notifications as read for repository: $repoName"
            & $ghPath api -X PUT "repos/$repoName/notifications" --field "last_read_at=$(Get-Date -Format s)Z" 2>$null
            Write-Log "Successfully marked all notifications as read for repository: $repoName"
        } catch {
            Write-Log "Failed to mark notifications as read for repository $repo.full_name. Error: $_"
        }
    }
} catch {
    Write-Log "Error marking notifications as read by repository: $_"
}

Write-Log "Script execution finished"

[DmitrySadovnikov]

I was able to remove it. This command gets all notifications, even read ones. It searches by name (Lido in this example) and calls the API to remove it.

gh api notifications\?all=true | jq -r '.[] | select(.subject.title | test("Lido"; "i")) | .id' | xargs -L1 -I{} gh api \
  --method DELETE \
  -H "Accept: application/vnd.github+json" \
  -H "X-GitHub-Api-Version: 2022-11-28" \
  /notifications/threads/{}

GitHub Doc

[godcong]

@DmitrySadovnikov

Thanks for the reply, but this still doesn't work.

The problem is that notifications?all=true contains no information about these repositories. Therefore, I cannot fix them using this method.

According to 178382, these appear to be scam projects that GitHub removed, but the notifications about them were not cleared.