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Gonna guess that a font was in use when the installer tried to overwrite it with a new version, so it got marked for replacement at the next available time, which is usually a reboot.
But it might have been the case that the deletion request was just taking a long time, or else something decided a reboot wasn't needed, eventually pulling the rug out from under the font.
Sure, the new font might have been written to the old filename, but the inode will have changed and any programs looking at the old inode will end up reading garbage (maybe being stopped from doing so by the kernel) or being confused because the file there is marked as deleted now.
Presto, no font-o. [][][][][][][][]