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!