It's labeled internally, I believe, as a season 1 skit. I've seen some examples of a new version of something superseding the old one's production code in some materials.
I've wondered about this (and debated whether to ask about it), if the versions of Rubber Duckie (and other song inserts that were retaped with the same character, like Cookie Monster singing "C is for Cookie" or Kermit singing "Bein' Green") were given distinctive titles to tell them apart (even if it's just something like "Ernie Sings Rubber Duckie - Version II") or if they list them the same/generically and the only way to tell which version it was was in the production code, run time, or episode number listed.
But I have recently read on the wiki that the Grover "g-growing" segment is listed as a season 1 sketch even though it has the blue Grover, which made me wonder what other segments have production codes for the wrong season (not counting if it was held over until the next season), and season two Rubber Duckie was the only one I really suspected.
Incidentally, in terms of production codes, I've noticed in script pages for the episode where Maria and Luis get married (which are pictured in the 40th anniversary book), there is one segment listed, "Little Things", with a season 20 production code, even though the script is for a season 19 episode. I wonder what was going on there.
Some sources say he voluntarily left because his time with the Muppets made traveling to New York for just one character (Ernie) was impractical.
It is interesting that, for the most part, they only had Steve perform Ernie on the show, plus occasions where he did Kermit (more rare on Sesame Street, and most of them came during the very end of the 1990s). I know he did perform Dr. Feel as well, and he performed some one-shot characters in Elmo in Grouchland and Cinderelmo.
Maybe they just had him do Ernie because they knew he could do it but The Jim Henson Company or whoever figured he'd be busier with other works of the company (though he seemed to be performing Ernie a lot in seasons 30-35) and didn't want to worry about him performing more recurring characters, though I'd like to think he could have done some one-shot characters during Steve's Sesame sessions.