Looking through the tgas, there are no stems for the flowers. There also isnt anything for the yellow part. It doesn't look very fitting for an ice-based stage.
I don't know if this will work but when you use the my music mod, your stage can get corrupted. Here is a code to reset green hill zone:
Green Hill Reset [Full Metal Kirby]
4A000000 9018CDEC
5A010000 00000598
14000000 000027F2
14000004 00541D32
14000008 000027F5
1400000C 00001D32
14000010 000027F3
14000014 00001D32
14000018 000027F4
1400001C 00001D32
14000020 000027F7
14000024 00001D32
14000028 000027F8
1400002C 00001D32
14000030 000027F9
14000034 00001D32
14000038 000027FA
1400003C 00001D32
14000040 000027FB
14000044 00001D32
14000048 000027FC
1400004C FFFF1D32
14000050 000027FD
14000054 00001D32
14000058 000027FE
1400005C FFFF1D32
E0000000 80008000
I think he wants to know where the texture file for the stems and center part of the flower are in the greenhill.pac
:>.>:...
You're right.., I thought he meant the stems for the flowers were gone in-game..
sorry!
Those are auto-colored polygons, there's not much you can do about changing them; they don't use textures.
Maybe try editing any color palette files you see?