I ran into a bug that may be the same as yours :

My data is on a different partition than the system.
I use symbolic links in the ~ directory to access these files.

e.g. /home/me/Download is a symbolic link to /media/DATA/me/Download/

When I try to delete a file from the Download folder, accessing it
through the symbolic link, I have a message that says (I translate)
'unable to move the file to the trash do you want to delete it
completely ?' or (using Thunar on Xubuntu 16.04) **"invalid cross-device
link"**

This is the same whether the data partition is EXT4 or NTFS formated.

When I access the file directly from the /media/DATA partition I can
move it into the trash normally.

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https://bugs.launchpad.net/bugs/1612708

Title:
  Symbolic Link does not work in 16.04 LTS as in 14.04 LTS

Status in colord package in Ubuntu:
  Confirmed

Bug description:
  Ubuntu 16.04.1 LTS

  colord:
    Installiert:           1.2.12-1ubuntu1
    Installationskandidat: 1.2.12-1ubuntu1
    Versionstabelle:
   *** 1.2.12-1ubuntu1 500
          500 http://de.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
          100 /var/lib/dpkg/status

  Under Ubuntu 14.04 LTS I have created NAS access by using 'gvfs-mount
  smb://nasdo/public'. It is linked to '/run/user/1000/gvfs/ als smb-
  share:server=nasdo,share=public' and I have created a Symbolic Link to
  this point with 'ln -s /run/user/1000/gvfs/smb-
  share\:server\=nasdo\,share\=public ~/nasdo_public'. Using this link
  folders, and files on the NAS have been accessable with r/w from
  Ubuntu 14.04 LTS. This is, what I expect from 16.04, too.

  Since I have upgraded to ubuntu 16.04 LTS a few days ago, all the
  links seem to be the same, but opening a file does not work. It comes
  to an input/output error. I can use the links to folders to navigate,
  but there is no chance to open e.g. an LibreOffice Calc Sheet, nor do
  I have access to mail folder via Thunderbird.

  Using gvfs-mount creates a shared folder in Nautilus called public.
  Using this way to access the NAS, and open the Calc file works with
  ubuntu 16.04 LTS fine.

  Locking to the syslog while trying to open a file creates the following 
entries:
  Aug 12 16:47:19 UDO systemd[1]: Started Hostname Service.
  Aug 12 16:47:22 UDO org.gtk.vfs.Daemon[3843]: ** (gvfsd:3924): WARNING **: 
dbus_mount_reply: Error from org.gtk.vfs.Mountable.mount(): Empfangen der 
Freigabenliste vom Server ist gescheitert: Verbindungsaufbau abgelehnt
  Aug 12 16:47:22 UDO org.gtk.vfs.Daemon[3843]: ** (process:8645): WARNING **: 
Couldn't create directory monitor on smb://x-gnome-default-workgroup/. Error: 
Der angegebene Ort ist nicht eingehängt
  Aug 12 16:47:25 UDO org.gtk.vfs.Daemon[3843]: ** (gvfsd:3924): WARNING **: 
dbus_mount_reply: Error from org.gtk.vfs.Mountable.mount(): Empfangen der 
Freigabenliste vom Server ist gescheitert: Verbindungsaufbau abgelehnt
  Aug 12 16:47:25 UDO org.gtk.vfs.Daemon[3843]: ** (process:8663): WARNING **: 
Couldn't create directory monitor on smb://x-gnome-default-workgroup/. Error: 
Der angegebene Ort ist nicht eingehängt
  Aug 12 16:47:48 UDO systemd[1]: Started CUPS Scheduler.
  Aug 12 16:47:48 UDO colord[2727]: (colord:2727): Cd-WARNING **: failed to get 
session [pid 8722]: Kein passendes Gerät bzw. keine passende Adresse gefunden
  Aug 12 16:47:48 UDO colord[2727]: (colord:2727): Cd-WARNING **: failed to get 
session [pid 8722]: Kein passendes Gerät bzw. keine passende Adresse gefunden
  Aug 12 16:50:15 UDO systemd[1]: Started CUPS Scheduler.
  Aug 12 16:50:15 UDO colord[2727]: (colord:2727): Cd-WARNING **: failed to get 
session [pid 8842]: Kein passendes Gerät bzw. keine passende Adresse gefunden
  Aug 12 16:50:15 UDO colord[2727]: (colord:2727): Cd-WARNING **: failed to get 
session [pid 8842]: Kein passendes Gerät bzw. keine passende Adresse gefunden
  Aug 12 16:54:32 UDO systemd[1]: Started CUPS Scheduler.
  Aug 12 16:54:32 UDO colord[2727]: (colord:2727): Cd-WARNING **: failed to get 
session [pid 8936]: Kein passendes Gerät bzw. keine passende Adresse gefunden
  Aug 12 16:54:32 UDO colord[2727]: (colord:2727): Cd-WARNING **: failed to get 
session [pid 8936]: Kein passendes Gerät bzw. keine passende Adresse gefunden
  Aug 12 16:55:01 UDO dbus[2427]: [system] Activating via systemd: service 
name='org.freedesktop.hostname1' unit='dbus-org.freedesktop.hostname1.service'
  Aug 12 16:55:01 UDO systemd[1]: Starting Hostname Service...
  Aug 12 16:55:01 UDO dbus[2427]: [system] Successfully activated service 
'org.freedesktop.hostname1'
  Aug 12 16:55:01 UDO systemd[1]: Started Hostname Service.

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