In DKC2, both types of Squawks are different objects and can be placed together in the same level. Whereas In DKC3, there is a flag that determines whether a level will have the ordinary green Squawks or purple Squawks.
Every level/area has a "header" of sorts that contains several bytes that affect things such as the palette, music, entry positions and so on. There are also six miscellaneous parameter bytes in each header that affect other things. Part of the fifth parameter byte determines whether a level will use normal Squawks or purple Squawks. Setting or clearing bit 0x10 of this byte will enable or disable purple Squawks in that particular level.
Refer to
this document. It contains offsets for the headers of most levels, descriptions of most of the used values and a few other things.
Use a hex editor. The provided offsets should be correct for the USA version of the game; other versions may be slightly different.