Summary

A customer got the following error for removing a sub-site.

PS C:\Temp> Remove-PnPWeb -Identity testcaa -Force
Remove-PnPWeb : The attempted operation is prohibited because it exceeds the list view threshold.
At line:1 char:1
+ Remove-PnPWeb -Identity vacaa -Force
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : WriteError: (:) [Remove-PnPWeb], ServerException
    + FullyQualifiedErrorId : EXCEPTION,PnP.PowerShell.Commands.RemoveWeb

PS C:\Temp>

Clearly, the issue was due to a large list or lists present in the sub-site. Since the entire subsite needs to be deleted with the large list, to eliminate the above error the large list must be deleted first.

The following code can be useful to remove the items from the large list and it allowed to delete the list. Once all large lists were deleted the subsite was successfully deleted.

$action = "Delete"
# TODO Change your site or subsite URL
$siteUrl = https://[YOUR TENANT].sharepoint.com/sites/Contoso/testcaa
# TODO Change the list name 
$listName = "Contoso Community Care Data" 
$ErrorActionPreference="Stop"
Connect-PnPOnline –Url $siteUrl -UseWebLogin
$Stoploop = $false
[int]$Retrycount = "0"

write-host $("Start time " + (Get-Date))
do {
  try {

    if($action -eq "Delete")
    {
      $listItems= Get-PnPListItem -List $listName -Fields "ID" -PageSize 1000  
      $itemIds = $lisItems | Foreach {$_.Id}
      $itemCount = $listItems.Count
      while($itemCount -gt 0)
      {
        $batch = New-PnPBatch
        #delete in batches of 1000, 
        #if itemcount is less than 1000 , all will be deleted 
        if($itemCount -lt 1000)
        {
          $noDeletions = 0
        }
        else
        {
          $noDeletions = $itemCount -1000
        }
        for($i=$itemCount-1;$i -ge $noDeletions;$i--)
        {
          Remove-PnPListItem -List $listName -Identity $listItems[$i].Id -Batch $batch 
        }
        Invoke-PnPBatch -Batch $batch
        $itemCount = $itemCount-1000
     }
   }
   Write-Host "Job completed"
   $Stoploop = $true
  }

  catch {

    if ($Retrycount -gt 3){

       Write-Host "Could not send Information after 3 retrys."

       $Stoploop = $true

    }

    else {

      Write-Host "Could not send Information retrying in 30 seconds..."

      Start-Sleep -Seconds 30

      Connect-PnPOnline –Url $siteUrl -interactive

      $Retrycount = $Retrycount + 1

    }
  }
}
While ($Stoploop -eq $false)
write-host $("End time " + (Get-Date)) 

Conclusion

To delete any site the large lists items and list must be deleted first. Once that is done the site or subsite can be deleted.

Reference:

PnP Batch Add or Delete items from very large list, i.e. more than 300k items – Microsoft Tech Community

The fastest way to create SharePoint list items – Waldek Mastykarz