Why are my images no longer in their folders?

My photos are all within lightroom, all 24,000+ images.  I had them organized them in folders by year, month and date.  For some reason, my folders for April 2014 were being downloaded in another place in the library.  I was having to move them down in LR to their proper place in the year and month, each time I downloaded images. So, the other day, I went over, in the Library, to the appropriate place in the right hand column and selected the spot when I wanted them to go.  Then, presto magic, most of the photos disappeared from their folders.  The photos remain in LR, just not in their appropriate folders.  In my picture file, all images are still in the folders where they belong.  What happened?  What did I do? How can I get them back into their folders? 

I wanted to change the destination of the photos.  You do this along the
top of the import page where it says, "Select a destination," but you
find the place you want it to go on the left side.
No, this is wrong. You do indeed select the destination at the top right of the Import dialog but you see either the same destination folder or a sub-folder in it, if you have chosen that option, on the bottom right. The left side is only sources from which photos can be copied or added.
When the images were downloaded, I went over to the right side and I believe actually found all the photos were gone.
If the photos were downloaded (something which is not certain from your description) the Import dialog would have closed, putting you back in the Library module. But the right side panel of the Library shows only a histogram, Quick Develop, keywording tools, metadata readouts, etc., so it is hardly surprising that you did not find folders and image files there. They are found on the left.
I went back, in LR, on the right side [?] to my Root Folder, in which all of the images in their folders are stored under Pictures and set up an import.
Imported using the "Add" option in order to catalog them in place or by making copies or moving them to another location?
The images all returned to LR, but they were no longer organized in their folders.
Perhaps because of not understanding the Import interface you moved or copied them to a different destination and it is this alternate or second location that the catalog now refers to.
Does this clarify?
No, I'm afraid not. Maybe if you spent a bit more time understanding the layout and structure of LR's UI, you could explain your problem better.

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