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The installer just has a specific file/reg location, where it stores files to delete at the next reboot. Then, the uninstaller deletes the files, or, if started before reboot complains about the fact, that there are files in the setup, which will be affected by the next startup-delete-process.
there is no real "mark" (on a filesystem-level, or whatever you thought about), its just an information the installer itself uses and stores somewhere.
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