Best way is to remove them with Powershell. For example:
If you've deleted them from C:\Program Files\WindowsApps you'd have to do an in-place upgrade to add them back (or possibly try adding them back from the Store ) and then remove them again with Powershell.
# Remove for users
Get-AppxPackage -Name $app -AllUsers | Remove-AppxPackage
# Delete from WindowsApps
Get-AppXProvisionedPackage -Online |
where DisplayName -EQ $app |