Restoring a Bioassayset or Transformation restores all child bioassay sets and transformations but not the parents
If you for example have marked one part of the analysis for deletion and try to restore the topmost item, all items below it are also restored. On the other hand, it you restore a leaf it's parents will not be restored. I think it should work the other way around. If you restore an item in the analysis tree it's parents should also be restored, but not the children.