I forgot to mention that before I drag take 2 back, I have to actually trim it or else CH will not break the relationship with take 1.
When you have created the takes they are all selected so this is why the Trim operation works on all of them. To stop this happening simply deselect the takes that you don't want to be affected by the Trim. It may be worth filing a feature request to have the selected takes be more obvious as visually I don't think it's clear enough that they are selected.
Hope this helps.
Try Edit > Split to break a take into more segments - I think that will solve your issue.
In general, the top take always "shadows" the lower takes because the typical workflow is that users tend to fix or make something better with each consecutive take.