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Something very similar has happened to me once or twice when menu bar items were present but somehow invisible, and positioning my cursor where they should be seemed to revive them!
Are you expecting other icons in the gap? If not, does this gap appear when starting the Finder, with icons shuffling about for the first few seconds? Have you tried Force Quitting/relaunching the Finder (from the Apple Menu, for instance) and seen if that sorts it out?
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