How do I use 'notify-send' to immediately replace an existing notification?

You can, but you must use a patched libnotify to do so

notify-send does not have the capability to replace existing notifications before they have timed out (or disappeared). This is a known bug. However, a commenter on the bug report has posted a patch to fix it.

Installing the patched libnotify-bin from PPA

I have created a patched version of the libnotify-bin package which allows replacements in my PPA. Currently it's for Ubuntu 12.04 only, but if you need it for any other currently supported release, please post a comment and I will try my best to make it available.

To install, open a terminal and:

sudo apt-add-repository ppa:izx/askubuntu
sudo apt-get update
sudo apt-get install libnotify-bin

How to use the replacement capabilities

The patched notify-send includes two new switches, -p (or --print-id ), and -r (or --replace-id ). The --help describes them as:

  -p, --print-id                    Print the notification ID.
  -r, --replace-id=REPLACE_ID       The ID of the notification to replace.

• With -p, each notify-send will return an ID N (number/integer).
• Issuing another notify-send with -r N will replace the previous notification immediately.

• For example, for bash, you can save the ID from notify-send -p ... with:

  NID=$(notify-send -p "MESSAGE-1")
  

  and then replace it with:

  notify-send -r $NID "MESSAGE-2"
  

• You can recursively use both -p and -r in a script, as long as the -r variable is initialized to 0 at the beginning.

• Here's a simple script that shows notifications counting from 0 to 100 at half-second intervals:

  #!/bin/bash
  
  NID=0
  
  for i in {0..100..10}
      do
            NID=$(notify-send -p -r $NID $i)
            sleep 0.5
      done
  

You can use the "synchronous" hint to create a "confirmation" notification that will replace previous confirmation notifications. For example:

notify-send "Message" -h string:x-canonical-private-synchronous:anything

The "x-canonical-private-synchronous" hint is specified in this document. To specify a hint, use -h type:name:value. The type here is string, name is x-canonical-private-synchronous, and it seems that the value can be whatever you want.

So if your first notification is created with that hint and the second is as well, the second will immediately replace the first. (See Animations and Durations in the documentation, in the column for "confirmation bubbles".)

X-ref:
How to force a new Notification in notify-osd to show up without waiting for the earlier one to exit?

without patches you can simply do

#!/bin/bash

for i in {0..100..10}
    do
          killall notify-osd
          notify-send "testing" $i
          sleep 1
    done

Bookmark:
How do I use 'notify-send' to immediately replace an existing notification?

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Sends an error notify-osd(2592): Operation not permitted. What does that mean?

It may mean that privileges are inadequate requiring:

sudo killall notify-osd