It was Desmonds wish to have an assistant to speak the most difficult lines because he was starting to have even more trouble with all the technical things in the script. He had wished assistant since Goldeneye.
He was going to come back as Q in Die Another Day, I remember him saying something like this in an interview about week before he died that "I am looking forward to have some funny gags in the next movie with John Cleese"

I think Desmond Llewelyn was going to be Q as long as he was alive and the producers wanted him so he said in an interview, I think John Cleese still would have been R but may have had a bigger role than Desmond Llewelyn.
I'm not sure why they brought in Cleese anyway, was it just so Desmond Llewelyn wouldn't have to do anything too demanding if the scripts called for it? Such as having to visit Bond on the job. Or was it to provide some continuity in case anything happened to Llewelyn?
The world is your lobster.

loved the exit, it was a euphemism for his ending of playing Q but also made sense in the movie re. Bond. Brilliant!

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Well, they were considering replacing Q as early as the first script for "Tomorrow Never Dies," so who knows?

John Cleese's character isn't named 'R'. It also 'Q'. Q stands for Quartermaster.
Bond only jokes about 'R' coming after 'Q'. But in 'Die Another Day' he is called 'Q'.
Desmond's characters was named Major Boothroyd. 'Q' is only the position like 'M'.

yeahthey put R in there knowing that he was retiring from the roleand in my opinion one of the best exits in a movie with his line and dissappearance

Q wasn't in Live and Let Die
ClarkF1

He would've had a cameo appearance in Die another Day if he was still alive, as he did retire from the role in 1999.

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He played in every single Bond except for the first I think, why would he not have kept playing the part?
It's not a lie if you believe it.