Weird and hidden references after retargeting animations.

I recently retargeted around 7,000 animation sequences (plus some blendspaces) to the MetaHuman skeleton. Bulk retargeting worked overall, but plenty of strange references remain. When attempting to migrate only the animation sequences, they still carry hidden links to the original skeletal mesh used before retargeting.

Some issues were easy to fix, like references from the animation compression plugin, which went away after swapping the skeleton from MetaHuman to the MetaHuman skeleton (yup weird animations). But other references are buried deeper and harder to track down.

I wrote recursive C++ function, that prints out every reference an object holds. All of those point correctly to the MetaHuman folder, yet Unreal still prompts to migrate the old skeleton along with the assets.

Yes, the old folder can just be unchecked during migration, but the concern is whether something important might be broken in the process.

So the question is: Is there a proper way to bulk retarget a huge set of animations without leaving behind hidden or hard-to-find references?

Retargeting is definitely better than it used to be, but there still seem to be layers of strange leftovers.