With some uncertainty:
Beethoven: Str4 13 Bb Op130: Original finale Große Fuge later replaced by a daintier allegro.
Mahler: Symphony 1, in its earlier forms (1889, 1893—4) having its Blumine movement.
Milhaud: Str4 14 —5 , ad lib performed simultaneously as octet ; all 3 works sharing opus number 291.
(From thread Levels in the structure of works, @derobert looking “for works that are part-of more than one work”.)
Atterberg: Symphony 2 (originally in 2 movements and as such expressly content; later added a finale III. Allegro con fuoco)
Ben Johnston: Sonata for Microtonal Piano / Grindlemusic
This “Janus-faced work” comes from reördering the same 3 of 4 movements:
Piano Sonata:
- “sonata-allegro”
- “scherzo”
- “slow movement”
- “finale”
Grindlemusic:
- Premises [“finale”]
- Questions [“sonata-allegro”]
- Soul Music [“slow movement”]
- Mood Music [“scherzo”]
In opera also numerous cases of number revision (Fidelio/Leonore), arias and else going in and out of score, sung recitative replacing originally spoken dialogue (Medea, Carmen), notably differing versions (Don Carlos), …