Have this problem reported last year, and got a confirmed bug 1612708.

Was in the meantime back to 14.04 LTS, but now upgraded to 16.04.2 LTS
because some drivers have been available only for this release.

The problem in 16.04.2 LTS still exists. Very sad :-(

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https://bugs.launchpad.net/bugs/1598183

Title:
  Operation not permitted while writing to symlinked fuse locations

Status in gvfs:
  Confirmed
Status in gvfs package in Ubuntu:
  Confirmed
Status in gvfs source package in Xenial:
  Confirmed

Bug description:
  Affected releases:
  Ubuntu from 14.10+ (14.04 was working fine) 

  Steps to reproduce:
  1. Setup a gvfs mount (I used smb and sftp shares configured via nautilus).
  2. Create a symlink to the fuse-mounted location e.g.
  cd ~/Desktop; ln -sf 
/run/user/1000/gvfs/smb-share:server=10.0.20.6,share=share1/symlinktest
  3. Navigate with nautilus to the symlinked location, open a file available 
there with e.g. gedit or libreofficeand try to save it.

  Expected result:
  File is saved.

  Actual result:
  An enigmatic error message is displayed
  (Cannot handle "file:" locations in write mode - for gedit, or "General 
input/output error while accessing <path>" for libreoffice).

  The problems started with commit
  548ba46c2ba51c4ec5b0dd8442b476f3a2a7000b fuse: Don't g_file_append_to
  unless O_APPEND is given. Reverting it makes the issue disappear.

  I have rebuild gvfs enabling debugging (#define DEBUG_ENABLED 1) and here is 
what I got in ~/vfs.debug:
  # accessing via symlink
  vfs_open: /smb-share:server=10.0.20.6,share=share1/grouptest/symlinktest/test
  open_common: flags=500002
  vfs_open: -> Operation not supported
  # accessing via /run/user/(...)
  vfs_open: /smb-share:server=10.0.20.6,share=share1/grouptest/symlinktest/test
  open_common: flags=1100000
  setup_input_stream: have stream
  setup_input_stream: doing read
  vfs_open: -> Success

  For reasons beyond my understanding the flags are different while
  accessing the file via the default gvfs-mountpoint causing the
  execusion to skip the modified section of client/gvfsdfusedaemon.c
  (returning -ENOTSUP).

  I am attaching the full vfs.debug created.
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