I can reproduce this bug on 16.10 Nautilus version is 3.20.3 following Michael 
Black's steps, but there is small mistake:
it should be :
cd Desktop instead of "cd ../Desktop"

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https://bugs.launchpad.net/bugs/1656370

Title:
  merging symbolic link with target folder of same name destroys folder

Status in nautilus package in Ubuntu:
  New

Bug description:
  I recently lost a directory full of valuable files.  I'm running
  ubuntu 16.04 and using nautilus 3.14.3

  Here's how to replicate this bug.  From a terminal window starting in
  my home directory:

  mkdir useful
  cd useful
  touch stuff1.txt
  touch stuff2.txt

  cd ../Desktop
  ln -s ../useful/ useful

  Now I have a symbolic link on my desktop "useful" that links to
  directory "useful" containing two files.

  From nautilus:

  - Go to Desktop, select the link useful
  - press Ctrl-X to copy
  - Go to Home
  - press Ctrl-V to paste
  - dialog box appears: Merge folder "useful"
  - press Merge button (the default)

  directory useful has now been replaced with a symbolic link pointing
  to itself, and all its contents are gone.

  Now in nautilus I press Ctrl-Z to undo.  Symbolic link "useful"
  reappears on the Desktop, but the target folder is not reconstructed.

  Why is this a important bug:

  1. Merge dialog gives no indication that the source is a symbolic
  link.  Instead it asks the user if wants to merge the files in two
  folders.

  2. Continuing with the merge is the default option.

  3. After the merge the symbolic link survives and the folder and its
  contents are utterly gone.  They cannot be found in the trash.

  4. Undo does not restore the folder or its files, just relocates the
  symbolic link.

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