Keeping Layers in placed Items - or other workarounds

Hey guys, 
I have encountered an issue that i cant wrap my head around. I have a Script that creates files and saves them, opens a new File and places them on it for our printer. After changes in my workflow i need specific parameters saved in my files -  i planned to do it through layers and layernames. Unfortunately after you place and embed a file all the layer and vector data is lost.  I have 2 workarounds for this in my mind:

1.  I color elements and go through all pathElements on the big file and move them to layers - but this is resource heavy and the layer management is also bound to code changes.
   
   
2.  I open the single files and copy them in the big file with the "Remember Layers on Paste" option - but its time consuming and i would need to add bounding boxes for the files, which the placedItem element already has. Also in order to position them i wound need to group the elements, which again destroys the layers.
   
   Am I missing something or is there maybe an easier and more elegant solution to this problem?
   
   Thanks in advance!