Since the Mee-Mee "Maybe something died" was in the workprint, which of course dates from after Mee-Mee being removed from the film, it was obviously intended to be in Williams' final cut. The reason it's such a discrepancy is because it's still a pencil test of Tissa David's animation from c. 1977-80, at a time in which Mee-Mee was still in the film, and the scene. In the workprint, this late-70s animation was featured as a placeholder; new animation would obviously have been done to replace all of those shots, to remove Mee-Mee, redesign Yum-Yum, or replace Mee-Mee with Yum-Yum.
Since Hilary Pritchard's voices for Mee-Mee and Yum-Yum were so similar, the original dialogue was obviously edited down (or re-recorded? The mouth movements sometimes seem off...) to turn it from a scene with Mee-Mee and Yum-Yum into a scene with just Yum-Yum. The "Maybe something died" would have, in a finished version, been uttered by a reanimated Yum-Yum (with correct design).
In fact, in Fred Calvert's workprint (and in the Recobbled Cut), the shot of Yum-Yum holding her nose after smelling the Thief is a pencil test of a reanimated (by Williams' crew) version (obviously done / filmed after the Williams workprint we have, but before his "forced departure"), in which Yum-Yum is drawn with her finalized design, and Mee-Mee is absolutely gone. (For those who have only seen the Recobbled Cut, the workprint instead has Tissa David's late-70s animation in this spot, with the earlier Yum-Yum design, and Mee-Mee in the bath next to her.)
Oh, if only we could find the last Williams workprint (the one from which Calvert got all those new pencil tests and finished shots for *his* workprint)...it would clear a lot of this stuff up...