I was organizing folders on my Desktop by moving them to Documents.  When I moved the folder I didn’t check to see if there was a folder with the same name in Documents.
 
There was a folder with the same name in Documents.  When I moved the folder it disappeared from Desktop as expected, but the folder (and its files) did not appear in any form in Documents.  All of the files, constituting several semesters’ worth of work disappeared.
 
I have actually been able to reproduce the issue:
I created two folders with identical names (TEST), one folder on my Desktop and one folder in Documents.
I then saved a Word doc in the folder on my desk top called Test A and a Word doc in the folder in Documents called Test X.
In File Explorer I dragged the TEST folder with the Word doc in it from my Desktop to Documents.
I was not informed of duplicate folders by Windows.
The TEST folder on my Desktop disappeared (as expected).
When I opened the TEST folder in Documents the only file in it was Test X.
File Test A originally in the TEST folder on my Desktop disappeared.
Any suggestions on recovery?

The makers of Ccleaner make a free app called Recuva. It's pretty good at finding lost files, even those that went through the recycle bin.

That's scary. Haven't seen those kinds of problems since DOS 4.0 and Netware days when files would be randomly corrupted.
 
I have, however, had files simply not be moved via dragging. I'd get the little animation, but nothing was copied. Fortunately, the original files were intact. Never been a big fan of drag 'n drop - too easy to screw up, e.g. accidentally dropping files into a subdirectory. Most of the time I use XCOPY or MOVE commands in a DOS window. That's never failed me.

I just tried your replicated error, and Win10 automatically combined/merged the two TEST folders in the Documents folder, but keeping BOTH word files.  So, not sure what's going on with your Windows build.  As for not seeing the "warning," you can change that by going into FOLDER OPTIONS and unchecking the "Hide Folder Merge Conflicts" option in the VIEW tab.
 

ampfixer
The makers of Ccleaner make a free app called Recuva. It's pretty good at finding lost files, even those that went through the recycle bin.

+1 on Recuva.  I've used it with success.  The trick is to use it early, immediately after the file loss.

I just tried this and like 2:34AM, Windows automatically merged the two folders and kept a copy of each document in the new merged folder. So I don't know where your missing file is going. 
 
However I was surprised that there was no merge warning by default. Did that change? I could swear that Windows always warned the user if moving a folder or file to a location where the same name folder or file exists. 

sharke
I just tried this and like 2:34AM, Windows automatically merged the two folders and kept a copy of each document in the new merged folder. So I don't know where your missing file is going. 
 
However I was surprised that there was no merge warning by default. Did that change? I could swear that Windows always warned the user if moving a folder or file to a location where the same name folder or file exists. 

That seems to come and go, sometimes I'll get the warning, sometimes Windows will just add a (1) to the file name.

To add to the above, if you have a folder called "WHATEVER" and then assign your Pictures library to it (by right-clicking, selecting Properties, then changing the destination - an excellent way to get personal data off your OS drive by the way), you will see the folder show up as "Pictures" even though it's still called "WHATEVER" behind the scenes.
 
I've also run into the situation where the library folders you see from File Explorer are NOT the actual ones under your "User" directory!  Gee, that's not confusing at all, ya? 
 
When you add that to the fact that Windows likes to keep certain personal data buried in hidden folders on your OS drive that you can't see by default and typically don't even know exist (mail files for example), well...  Windows is a mess!

craigb
When you add that to the fact that Windows likes to keep certain personal data buried in hidden folders on your OS drive that you can't see by default and typically don't even know exist (mail files for example), well...  Windows is a mess!

The irony is that by trying to make things appear "simple" for the most absolutely clueless users, they have made it a confusing mess for anyone who knows enough to navigate a folder tree. 

Unfortunately, it did not (or at least it did not successfully) merge the folders and it did not rename it (1).
 
If I go into File Explorer and then to Quick Access it shows under Recent Files both Word Docs, Test A and Test X, BUT they both appear as if they are in - "This PC\Documents\TEST".
 
Test A does not show up in Quick Access in - "This PC\Desktop\TEST" - where it originated.
 
When I click on Test X while in Quick Access -> Recent Files it opens in Word.
When I click on Test A while in Quick Access -> Recent Files I get "This File Could Not Be Found".
 
This suggests to me that Windows attempts to merge the folders containing the files but somehow corrupts them in the process??? 
 
I will try Recuva later tonight and let you know how it goes.
 
Here is my Laptop OS info:
 
Edition - Windows 10 Home
Version - 1703
OS Build - 15063.674
It is a 64 bit OS that originally came with Windows 7.  It was a bear installing 10.
 

bitflipper
Never been a big fan of drag 'n drop - too easy to screw up, e.g. accidentally dropping files into a subdirectory. 

 
@OP My first thought was if this is what had happened ? It would explain the lack of dupe file warning. Silly question maybe, but have you tried running a search for it or just assumed that it's gone because it isn't where you think you put it? Yeah, I know....but we all sometimes miss what is staring us in the face.
 
 
 
 
 
 
 
 
 
Thinks to self...........I wonder who is going to be first to mention back-up copies ?