What those reboots normally do is replacing files that are currently in use. The patch writes the files that are to be overwritten into a special registry key. Then, upon reboot, the operating system replaces those files with the updated ones as specified in the registry beofre the files are loaded.
See the UDF UpdateFileOnReboot - Schedules a file to be replaced on reboot
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There are two types of vessels, submarines and targets.
