Merging models after Horizontal transition

I created a child model from a parent model using the horizontal transition. The child model contains certain components from the parent but not all of them (logical functions and logical components) .
When I add new elements to the child and try to push them to the parent, there’s an issue with the “containers”. For example , when you create a new function it is contained in the folder “Logical Functions” on the project explorer. However, when I try to transfer my new function using the diff/merge window, I get duplicate folders because the one in the Child and the one in the Parent don’t have matching IDs or SIDs.
It’s like the transition only linked the components from the two models but not the folders that contains those components.
I wanted to know if there’s a way for me to link the “containers” during the initial transition so that when I compare the two models after some changes, the new elements will be transferred to the right directory without deleting elements that don’t have a match.
Thank you .