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This site already has a couple of good answers explaining that, after NASA returned to sequentially numbering Space Shuttle missions following STS-51-L, some flights were internally written with an R appended to avoid duplicating old designations. But neither of them say what the R stands for, and I haven't been able to find a reliable source.

As of this writing Wikipedia says that it stood for "Rookie", but I believe that's based on a misreading of this document, which uses e.g. R2 to refer to Robert Crippen, the second rookie astronaut to fly on the shuttle (see page 1-1 for definition (the 13th page of the pdf)).

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    $\begingroup$ I see that you already looked at the answers I was going to link. As far as I know, the R stands for Reflight, but I am not sure there is a reference for that. I'll take a deep dive though. The Wikipedia "rookie" thing is ridiculous. $\endgroup$ Commented Feb 14, 2022 at 19:43
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    $\begingroup$ Wikipedia's list of shuttle missions agrees it is "reflight", and points to a citation in Jenkins, which will almost certainly have chapter and verse. I'll remove the "rookie" comment from the WP STS-32 page. $\endgroup$ Commented Feb 14, 2022 at 21:32
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    $\begingroup$ Got it: Jenkins does indeed say "Reflight" explicitly. I'll type it up tomorrow unless @OrganicMarble wants to answer first, I think you have priority :-) $\endgroup$ Commented Feb 14, 2022 at 22:01
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    $\begingroup$ @OrganicMarble and done, with a present of a completely unexpected third numbering system :-) $\endgroup$ Commented Feb 14, 2022 at 23:56
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    $\begingroup$ @Andrew spectacular answer! $\endgroup$ Commented Feb 15, 2022 at 0:05

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The confusing alphanumeric description scheme was dropped after the Challenger accident in 1986, the program returning to the original 'STS' numbering system. This, however, also caused some problems since NASA decided that the first flight after the accident would be STS-26 (Challenger was the 25th flight launched). To overcome the problems of having two 'STS-26' missions (Flight 19/51-F before the accident, one after), the mission was carried internal to NASA as STS-26R, the 'R' signifying 'reflight'. The 'R' suffix was added to missions through STS-33R, the number carried internally by Challenger.

Jenkins, DR (2001). Space Shuttle: The History of the National Space Transportation System, p.294 [emphasis mine]

Unfortunately, this is an explanatory note at the start of a table of missions, and it doesn't really go into any detail. There is a citation pointing to various sources including the Space Shuttle Mission Chronology (1999), but it seems likely this refers to the data in the following table rather than the specific "R[eflight]" note. However, Jenkins is pretty comprehensive and well-researched, and I think can be taken as authoritative here.

There is a similar comment in Iliff, K. (2004). From Runway to Orbit, NASA SP-4109, p.278

The mission designations were rethought after the Challenger accident, and they did away with the 61-C type of classification. They went back to having it named simply as an STS mission. It was getting close to what we had done, but unfortunately they didn’t do them all in exactly the same order, even early in the program. In the first five or six flights, they flew STS-29 and STS-30 before STS-28, so we continued to use our designation of STS-26 for the first flight after the Challenger accident, which was going to be a Discovery flight flown by Rick Hauck and Dick Covey. Its official designation was STS-26R, the “R” stood for re-flight to make it clear that it was flown after the Challenger accident and the new STS designation system. I will use the official Shuttle designations for all flights after STS-26R to avoid adding confusion.

As an aside, his comment about "what we had done" seems to refer back to a third system used internally for analysis at Dryden and perhaps elsewhere, but which presumably was not being used anywhere in the actual launch workflow: just number them in the sequence they actually happened, ignoring everything up to that point, and not skipping any numbers. He described it a little earlier in the text:

After STS-9, the designations for the various Shuttle flights started to get very confusing, because up to that time the flight number and the STS number were the same. [...] Those of us doing the support for the vehicle, to make our databases more understandable to us and make sure we weren’t missing pieces, continued to call each subsequent flight by an STS flight number corresponding to the mission number.

There are later comments along the lines of "STS-11, officially known as STS-13 or 41-C" - it must have been a headache to keep these all straight, and I can see why they took the opportunity to re-synchronise with the official flight numbers!

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