Eu usei um utilitário chamado WhyReboot por motivos semelhantes várias vezes. Você pode encontrar uma maneira de usar esse utilitário ou seguir seus passos através dos artigos da MS KB que ele usou.
The simple, supported solution is to record an entry that will allow the file(s) to be copied, renamed, or deleted after the system reboots but before Windows loads (or any user applications start.) It is this method that most installer systems use.
I've investigated the methods used to request 'deferred' file operations after a reboot. It's not that tough, Microsoft provides sufficient documentation on their website:
* MS KB Article 140570 * MS KB Article 181345 * MS KB Article 184408 * MS KB Article 228930
There are other resources on the web (see related links, below)
I present to you the results of my curiosity and investigations: The WhyReboot utility.