Hi,
thank for coming back to me, but I think there is a misunderstanding. I'm happy to delete all contents of the parent folder just not the folder itself. This is because it's highly likely that permissions on this folder may be customised.
In order to keep only the folder, but delete its content, you can select the "Create folder on target machine" option from its properties, then go to its component and set the "Permanent" flag for it. In this case the folder itself will never be deleted from the machine.
If you want to remove it on a full uninstall, you can go to its "Operations" tab, check the "Remove folder" option on "Component uninstall" and use this condition for it:
NOT OLDPRODUCTS
Also, you made no mention of the removal of the IIS site and app pool problem
I mentioned that if you want to preserve the website configurations (including App Pools) during the upgrade, you can implement the solution from the "
Reinstalling dropping IIS settings" thread.
Best regards,
Eusebiu