Maybe a simple way is in LR to create a keyword for every collection and apply this keyword to all pictures in the collection.
Thus you may filter in dt on this keyword.
The technical reason why dt seems to break the hierarchy is LR puting the keywords multiple times in files. dt has no way of knowing how to handle this. Look for dc: subject and Lr:hierarchicalSubject.
You might use something like exiftool to clean up your files.
Need more details about exactly what you are doing to give more advise. For instance do you use .xmp files in LR, what kind of files do you migrate?