You need to add a file called unity_houdini.env in the /Assets folder of your Unity project (see here [www.sidefx.com])
Then in that file, add this variable HOUDINI_OTLSCAN_PATH=Path/To/HDAswith the path to your nested HDA (preferably in a shared location with your colleagues)
In my project I have a "main" hda with a couple of tools saved first as external hda and then added as embedded hda. Somehow Unity Engine keeps bumping the undefined nodes error as if they were still linked to their original locations.