I found the culprit, it is the entry [Internet Explorer *] from the latest Winapp2.ini. The merged FileKey4 is too aggressive, because it also cleans other cache folders that do not belong to Internet Explorer: FileKey4=%LocalAppData%\Microsoft\Windows\*Cache*|*|RECURSE This folder, for example, should not be cleaned up: %LocalAppData%\Microsoft\Windows\Caches