I tested this in an Ubuntu GNOME 16.10 GNOME 3.20 64-bit VM and found
that with the new update the issue goes away and the problem here is
fixed. Although it should be noted that after updating to the new
version it shows any mounted partitions with a long gobbledygook name in
the sidebar when running Nautilus as root.

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https://bugs.launchpad.net/bugs/1638245

Title:
  Files in the root of a folder on another partition symlinked to user's
  home cannot be moved to trash because of a patch in this package

Status in glib2.0 package in Ubuntu:
  Fix Released
Status in glib2.0 source package in Xenial:
  Confirmed
Status in glib2.0 source package in Yakkety:
  Fix Committed

Bug description:
  [ Description ]

  Can't trash files if the directory they are in is a symlink to another
  device

  [ QA ]

  Steps:
  1. Install system and partition disk into root and data partitions
  2. create ~/Data folder, and mount data partition on it
  3. create symlinks for ~/whatever/ to ~/Data/something/
  4. delete files directly inside ~/whatever/

  What happen:
  Then Nautilus says: "File can't be put in the trash. Do you want to delete it 
immediately?".

  What should happen:
  The files moved into Trash.

  [ Regression potential ]

  The proposed fix uses g_stat instead of g_stat to follow symlinks, so
  we know where to place the trash (you can't rename() across
  filesystems). If that is wrong, then it could regress trashing other
  kinds of files.

  [ Original ]

  I'm on Ubuntu 16.10 64-bit with libglib2.0-0 version 2.50.0-1.

  I've reported this bug (or marked as "it affects me") in a couple of
  other places before I've finally discovered that this is the package
  that's causing this problem, which unfortunately has been around for a
  couple of years now.

  This bug has been reported upstream as well, but it's just taking very
  very long to arrive at a decision and take action it seems.

  Apparently one of the patches
  (https://sources.debian.net/patches/glib2.0/2.50.1-1/0001-Fix-
  trashing-on-overlayfs.patch/) which is here
  
(https://launchpad.net/ubuntu/+archive/primary/+files/glib2.0_2.50.0-1.debian.tar.xz)
  to the original package which is here
  
(https://launchpad.net/ubuntu/+archive/primary/+files/glib2.0_2.50.0.orig.tar.xz)
  is the root cause of this annoying problem.

  As I prefer keeping one patition for the root filesystem (/), one
  partition for user settings (/home) and one partition for user data
  (Documents, Downloads, Drive, Music, Pictures, Public, Videos) which
  are simply symlinked to my home folder for ease of use, I cannot move
  any file to the trash in the root of these folders when I access them
  from my home folder or nautilus sidebar.

  This problem doesn't affect folders at all, nor any other files in
  subfolders, etc.

  So I was wondering if Ubuntu devs can leave out that particular patch
  when building this package for Ubuntu - if it doesn't cause more harm,
  which I doubt.

  Otherwise, I would appreciate if I could learn how to do it myself:
  how can I (as an end-user) compile the contents of
  "glib2.0_2.50.0.orig.tar.xz" with all the patches, etc. in
  "glib2.0_2.50.0-1.debian.tar.xz" except "0001-Fix-trashing-on-
  overlayfs.patch"?

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