Both Windows 95 and NT provide mechanisms for doing just this.
Under Win95 you use the WinInit.ini file. Create a [rename] section and
put in entries like "NewName.txt=OldName.txt" to have files renamed, or
"nil=OldName.txt" to have them deleted. Windows will perform this at
the next boot.
Under Windows NT, the MoveFileEx function has a parameter that allows
you to defer the move (or delete) until the next boot. It stores the
list of files to be processed in the registry.