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Updating metadata - whether that is Library, Map or Develop information - always makes a change in the Catalog,
Unless / until that change is written out to the file, the Catalog is all that has been changed.
If LR is set, or told, to write change out to file then the image file on disk can be updated (though not in the case of a virtual copy). In the case of a proprietary Raw file, only a separate "sidecar" XMP file will actually be modified by metadata changes, or in the first instance created as needed - except that date and time changes in particular, can update the proprietary Raw camera file too. Other file types hold and update their metadata, if written out, inside the single image file - DNG, JPG etc.
But there is no way AFAIK that LR can possibly change a file's actual folder location merely by writing out metadata to it.
HOWEVER in Lightroom we do not only see images presented by their folders, we also see Collections and Smart Collections.
For example. there may be a Smart Collection with selection criteria. This presents a subset of our image library, on the fly. based on what attributes the images have.
"Previous Import" is one such example, built in - its selection rule is: "having been in the most recently imported batch of images". Another Smart Collection may show only those images with a certain keyword. Another may show only those images that have been last worked on in LR within the last 10 days, or may use a combination of such rules.
So a subsequent import, or changing images in a way that's relevant to a selection rule, or merely the passage of time, can cause images to automatically disappear from / newly appear in these various smart views. There is no actual change to the physical location of any one of these images, and there is still only one of it.
This can be clarified using the "Go to Folder in Library" option, against a given image thumbnail.
Let me ask it another way:
I have updated a photo's metadata (capture date, etc.). It was previously placed in a folder dated in the year 1970, and should now be located in a new folder representing its actual date of capture (2012). After updating the metadata (Save Metadata to file) for the photo, the photo nonetheless resides in a folder dated 1970. Can Lightroom intelligently move such updated files to the correct date/folder?
OK, I see. The answer is no: there is unfortunately no way to auto-file images by moving them around according to rules, after they are imported; LR only offers an option to re-name those within their current folders.
If it's just a few, and you know which ones they are, you can just manually move them around within LR using the Folders panel.
Folders are merely a technical necessity; and their names and hierarchy can be arbitrary - Banana / 1970 / DonaldDuck / 2012 - and LR invests all that with no meaning; even if it happens to have a meaning to you.
However, in LR you could make a Smart Collection which selects images on whether their Capture Date was during 2012 or not. LR does understand this - Capture Date is systematic meaningful information, as "DonaldDuck" or "1970".folder naming are not.
So if you can ensure the desired capture date on each image before import, LR can easily use that to auto-file correctly by date during the import (move or copy).
That could either be done with a first temporary import to LR, writing the changed capture date along with other metadata back to the file, then removing it from the Catalog, then importing it again according to an auto-filing scheme - but that sounds to me laborious. Also some work you've unwittingly done to that first import such as adding to Collections, or making virtual copies, may then be lost.
So I would look instead at using a utility to directly alter the metadata on the image files FIRST, before they come into LR, for images where you know this is going to be an issue. For example: with film scans where the date of capture (scanning) needs to be changed to the date that your records show the photo was originally exposed, Something like http://u88.n24.queensu.ca/~bogdan/ "Exiftool GUI".
Also, of course... by means of the camera's, or the scanning software's, time and date and timezone setting!