I think I finally could reproduce this bug and I have reported it
upstream.

** Bug watch added: GNOME Bug Tracker #671250
   https://bugzilla.gnome.org/show_bug.cgi?id=671250

** Also affects: gedit via
   https://bugzilla.gnome.org/show_bug.cgi?id=671250
   Importance: Unknown
       Status: Unknown

** Changed in: gedit (Ubuntu)
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/893521

Title:
  gedit does not detect replaced open file

Status in Light-Weight Text Editor for Gnome:
  Unknown
Status in “gedit” package in Ubuntu:
  Confirmed

Bug description:
  Hello,

  You can reproduce this bug like this: 
  1. make two test files with the same name, but in two different directories 
and with different content
  2. make sure one of them is older than the other (in terms of creation and 
modification time, I didn't test which of those matters)
  3. open the newer file in gedit (do NOT close gedit from this point on)
  4. move the newer file to a different location
  5. move the older file to be in the same directory where the newer file was 
in step 3
  6. double click the older file in a file manager, the gedit window shows the 
contents of the newer file, i.e., it does not show the usual "File contents 
changed on disk, reload or cancel?" question. 

  Thank you!

  ProblemType: Bug
  DistroRelease: Ubuntu 10.10
  Package: gedit 2.30.3-1ubuntu1
  ProcVersionSignature: Ubuntu 2.6.35-31.62-generic 2.6.35.13
  Uname: Linux 2.6.35-31-generic x86_64
  NonfreeKernelModules: openafs
  Architecture: amd64
  Date: Tue Nov 22 11:18:45 2011
  ExecutablePath: /usr/bin/gedit
  InstallationMedia: Kubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100427)
  ProcEnviron:
   SHELL=/bin/bash
   LANG=en_US.UTF-8
  SourcePackage: gedit
  XsessionErrors:
   (gnome-power-manager:2087): Gtk-WARNING **: A floating object was finalized. 
This means that someone
   (polkit-gnome-authentication-agent-1:2267): GLib-CRITICAL **: 
g_once_init_leave: assertion `initialization_value != 0' failed

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