There is a way of removing just the flat keywords, leaving only the hierarchal keywords for Lightroom, but it is very laborious and you can only do it one file at a time. It will probably not be worthwhile doing it for a large batch of files with different keywords. But if you have a batch with the same keywords on a bulk ingest, you could remove the flat keywords in one image, then copy the resulting hierarchical keywords to a Metadata Template, then apply that template to the entire batch before importing into Lightroom.
To do this, you will need to use the excellent (and free) Notepad++. Make sure that the Compare plugin is installed (do this from Plugins ¦ Plugins Admin if not already installed).
Set up Notepad++ with two tabbed blank text windows, say for example New1.txt and New2.txt. It is easier if you look at them side by side: if you just see two tabs but only one window, right click on one tab header and select Move to Other View, then you will see two windows.
These are the steps:
1. In the PM Metadata (IPTC) Info panel, select all the keywords (ctrl-A), copy them, then past them (ctrl-V) into the New1.txt window in Notepad++.
2. In PM, return to the thumbnail and run Find and Replace (ctrl-shift-F). Run the ([\|]{1})|(\[(.*?)\]) grep string in Find and Replace to remove the structured keywords (if you look at Carl Seibert's article, you will see that this grep string was my suggestion).
3. Copy the resulting flat keywords from the PM Metadata (IPTC) Info panel and paste them into the New2.txt window in Notepad++.
4. Run the Compare plugin in Notepad ++. You will see the differing text highlighted in darker yellow (at least on my system) in the New1.txt window. That darker colouration represents the hierarchical keywords.
5. Select the block of hierarchical keywords, copy, then paste this over the flat keywords in the PM Metadata (IPTC) Info panel resulting from step 3. above (or delete them first and then paste into the blank keywords panel if you prefer).
You will now have only the hierarchical keywords. If you now save the metadata and import the images into Lightroom, the keywords will fit into your existing hierarchy without at the same time adding a load of unwanted flat keywords at the bottom of the Lightroom Keyword List.
It's all a bit long winded, but it should work (it does for me), if you really want to delete your flat keywords before importing into Lightroom.
I have not yet found a way of doing this via grep in PM alone, but if I do, I will post it on this forum. The process in Notepad++ could possibly be shortened via grep and/or a macro but it is simple enough anyway.
Graham