The Script:

# removeMissingResourcesInVmm.ps1
$noConfirmations=$false # $true = no confirmations, $false=confirm each stale record removal
function removeMissingResourcesInVmm($noConfirmations=$false){

  function confirmation($content,$testValue="I confirm",$maxAttempts=3){
    $confirmed=$false
    $cancelCondition=@('cancel','no','exit','nope')
    $attempts=0
    clear-host 
    write-host $($content|out-string).trim()
    write-host "`r`nPlease review this content for accuracy.`r`n"
    while ($attempts -le $maxAttempts){
        if($attempts++ -ge $maxAttempts){
            write-host "A maximum number of attempts have reached. No confirmations received!`r`n"
            break;
            }
        $userInput = Read-Host -Prompt "Please type in this value => $testValue <= to confirm. Input CANCEL to skip this item";
        if ($userInput.ToLower() -eq $testValue.ToLower()){
            $confirmed=$true;
            write-host "Confirmed!`r`n";
            break;                
        }elseif($userInput.tolower() -in $cancelCondition){
            write-host 'Cancel command received.'
            $confirmed=$false
            break
        }else{
            clear-host
            $content|write-host
            write-host "Attempt number $attempts of $maxAttempts`: $userInput does not match $testValue. Try again or Input CANCEL to skip this item`r`n"
            }
        }
    return $confirmed
  }

  try{
    write-host "Removing all stale ISO records of resources from the VMM Library"
    if($noConfirmations){
      Get-SCISO | where {$_.State -eq "missing"} | Remove-SCISO
    }else{
      $confirmed=confirmation "Remove orphaned ISO records from VMM"
      if($confirmed){
        Get-SCISO | where {$_.State -eq "missing"} | Remove-SCISO
      }else{
        write-warning "Skipped orphaned ISO records removal"
      }
    }
     
    write-host "Removing all stale Custom Script records of resources from the VMM Library"
    if($noConfirmations){
      Get-SCScript | where {$_.State -eq "missing"} | Remove-SCScript
    }else{
      $confirmed=confirmation "Remove orphaned Custom Script records from VMM"
      if($confirmed){
        Get-SCScript | where {$_.State -eq "missing"} | Remove-SCScript
      }else{
        write-warning "Skipped orphaned Custom Script records removal"
      }
    }
       
    write-host "Removing all stale Driver records of resources from the VMM Library"
    if($noConfirmations){
      Get-SCDriverPackage | where {$_.State -eq "missing"} | Remove-SCDriverPackage
    }else{
      $confirmed=confirmation "Remove orphaned Driver records from VMM"
      if($confirmed){
        Get-SCDriverPackage | where {$_.State -eq "missing"} | Remove-SCDriverPackage
      }else{
        write-warning "Skipped orphaned Driver records removal"
      }
    }
     
    write-host "Removing all stale Application records of resources from the VMM Library"
    if($noConfirmations){
      Get-SCApplicationPackage | where {$_.State -eq "missing"} | Remove-SCApplicationPackage
    }else{
      $confirmed=confirmation "Remove orphaned Application records from VMM"
      if($confirmed){
        Get-SCApplicationPackage | where {$_.State -eq "missing"} | Remove-SCApplicationPackage
      }else{
        write-warning "Skipped orphaned Application records removal"
      }
    }
     
    write-host "Removing all stale Custom Resource records of resources from the VMM Library"
    if($noConfirmations){
      Get-SCCustomResource | where {$_.State -eq "missing"} | Remove-SCCustomResource
    }else{
      $confirmed=confirmation "Remove orphaned Custom Resource records from VMM"
      if($confirmed){
        Get-SCCustomResource | where {$_.State -eq "missing"} | Remove-SCCustomResource
      }else{
        write-warning "Skipped orphaned Custom Resource records removal"
      }
    }
     
    write-host "Removing all stale Virtual Disk records of resources from the VMM Library"
    if($noConfirmations){
      Get-SCVirtualHardDisk | where {$_.State -eq "missing"} | Remove-SCVirtualHardDisk
    }else{
      $confirmed=confirmation "Remove orphaned Virtual Disk records from VMM"
      if($confirmed){
        Get-SCVirtualHardDisk | where {$_.State -eq "missing"} | Remove-SCVirtualHardDisk
      }else{
        write-warning "Skipped orphaned Virtual Disk records removal"
      }
    }  
      
    # Remove stale virtual machine records in VMM
    # Note: this does not delete the VMs from Hyper-V
    $missingVms=Get-SCVirtualMachine|?{$_.status -eq 'Missing'}  
    write-host "There are $($missingVms.count) missing VMs being detected."
    if($missingVms){
      foreach ($missingVm in $missingVms){
        if($noconfirmation){
          Remove-SCVirtualMachine -vm $missingVm -Force
        }else{
          $confirmed=confirmation "Remove VM $($missingVm.Name) from VMM"
          if($confirmed){
            Remove-SCVirtualMachine -vm $missingVm -Force
          }
        }
      }
    }else{
      write-host "There are no virtual machines with current status of 'missing' to clear." -ForegroundColor Green
    }
    return $true
  }catch{
    write-warning $_
    return $false
  }
}

removeMissingResourcesInVmm $noConfirmations

The Individual Commands:

# How to purge all erroneous records of resources from the VMM Library

# ISOs
Get-SCISO | where {$_.State -eq "missing"} | Remove-SCISO

# Custom Scripts
Get-SCScript | where {$_.State -eq "missing"} | Remove-SCScript

# Drivers
Get-SCDriverPackage | where {$_.State -eq "missing"} | Remove-SCDriverPackage

# Applications
Get-SCApplicationPackage | where {$_.State -eq "missing"} | Remove-SCApplicationPackage

# Custom Resources
Get-SCCustomResource | where {$_.State -eq "missing"} | Remove-SCCustomResource

# Virtual Disks
Get-SCVirtualHardDisk | where {$_.State -eq "missing"} | Remove-SCVirtualHardDisk

# Virtual Machines
# Remove stale virtual machine records in VMM: VMs with 
# Note: this does not delete the VMs from Hyper-V
$missingVms=Get-SCVirtualMachine|?{$_.status -eq 'Missing'}
function confirmation($content,$testValue="I confirm",$maxAttempts=3){
  $confirmed=$false
  $cancelCondition=@('cancel','no','exit','nope')
  $attempts=0
  clear-host 
  write-host $($content|out-string).trim()
  write-host "`r`nPlease review this content for accuracy.`r`n"
  while ($attempts -le $maxAttempts){
      if($attempts++ -ge $maxAttempts){
          write-host "A maximum number of attempts have reached. No confirmations received!`r`n"
          break;
          }
      $userInput = Read-Host -Prompt "Please type in this value => $testValue <= to confirm. Input CANCEL to skip this item";
      if ($userInput.ToLower() -eq $testValue.ToLower()){
          $confirmed=$true;
          write-host "Confirmed!`r`n";
          break;                
      }elseif($userInput.tolower() -in $cancelCondition){
          write-host 'Cancel command received.'
          $confirmed=$false
          break
      }else{
          clear-host
          $content|write-host
          write-host "Attempt number $attempts of $maxAttempts`: $userInput does not match $testValue. Try again or Input CANCEL to skip this item`r`n"
          }
      }
  return $confirmed
}

write-host "There are $($missingVms.count) missing VMs being detected."
foreach ($missingVm in $missingVms){
  $confirmed=confirmation "Remove VM $($missingVm.Name) from VMM"
  if($confirmed){
    Remove-SCVirtualMachine -vm $missingVm -Force
  }  
}

Sample Outputs:

PS C:\Windows\system32> Get-SCISO | where {$_.State -eq "missing"} | Remove-SCISO
Release               :
State                 : Missing
LibraryShareId        : 00000000-0000-0000-0000-000000000000
SharePath             : C:\Windows\system32\vmguest.iso
FileShare             :
Directory             : C:\Windows\system32
Size                  : 0
IsOrphaned            : False
FamilyName            :
Namespace             :
ReleaseTime           :
HostVolumeId          :
HostVolume            :
Classification        :
HostId                : 
HostType              : VMHost
HostName              : hv1.intranet.kimconnect.com
VMHost                : hv1.intranet.kimconnect.com
LibraryServer         :
CloudId               :
Cloud                 :
LibraryGroup          :
GrantedToList         : {}
UserRoleID            : 00000000-0000-0000-0000-000000000000
UserRole              :
Owner                 :
ObjectType            : ISO
Accessibility         : Public
Name                  : vmguest
IsViewOnly            : False
Description           :
AddedTime             : 7/22/1920 9:04:52 AM
ModifiedTime          : 7/22/1920 9:04:52 AM
Enabled               : True
MostRecentTask        :
ServerConnection      : Microsoft.SystemCenter.VirtualMachineManager.Remoting.ServerConnection
ID                    : 862c2f67-4c2c-4588-8a4f-16ed3c64366f
MarkedForDeletion     : True
IsFullyCached         : True
MostRecentTaskIfLocal :

### Truncated similar outputs ### 

# Checking custom resources
PS C:\Windows\system32> Get-SCCustomResource|select name
Name
----
SAV_x86_en-US_4.9.305.198.cr
WebDeploy_x86_en-US_3.1237.1764.cr
WebDeploy_x64_en-US_3.1237.1764.cr
SAV_x64_en-US_4.9.305.198.cr