Importing a mesh that changes the hierarchy of a related skeleton causes the animation retarget settings on the skeleton to be lost. This is because in UInterchangeSkeletalMeshFactory::EndImportAsset_GameThread we call USkeleton::RecreateBoneTree which clears the bone tree on the skeleton, clearing the retarget settings.
Ideally, we would remap the retarget settings from the previous bone map to the new bone map so that bones that exist in both the old and new hierarchy retain their retarget settings
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-342266 in the post.