The “replace batteries” message was incredibly annoying and intrusive. Not only that, but the text (different to your screenshot above) implied that one could either replace the batteries or use the app to control the box. Using the app simply caused the message to pop up continuously and never go away. As did using any other remote.
I had to get some life into the original remote and unpair it (press TV and << for 10 seconds) before the overly-intrusive message finally went away.
I don’t use the stock remote - I use a Logitech Harmony as often recommended on here.
EDIT: An even easier solution, given in the German section by Daniele, although this does require you have new batteries! You put the new batteries in the remote, use it once or twice until the message goes away, then take the batteries out. Done.