Ok, so that explains a few things, sorry for my earlier post, it really would be useful to have had all this info to start with. You've always run nautilus unknowingly, whenever you open a file-browser, e.g. to browse your home directory. Now that you know this, you should be able to use the reload button altair mentioned to update the display, which is also reloaded automatically as soon as you re-open the folder.
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