I had the same exact problem with 2 remote keys on my Harmony 650 remote. Both the "Guide" and the "Menu" buttons changed functions when upgrading to LE 9.0 (Kodi 18). The "Guide" button used to activate the context menu and the "Menu" button used to activate the Kodi "home" function. I had to reprogram the remote using the Logitech Harmony software to change the "Guide" key back to "DVD Menu", which is the context menu on Kodi. But now both the Guide and Menu keys do the same thing (Kodi context menu). I lost the "home" function and don't see that function mentioned in the Logitech Harmony software.
I'm also running an old 3rd gen Intel NUC
With Kodi 17.6 the Menu button was the "Home" button for Kodi. The Guide button was Kodi's "Context Menu"
With Kodi 18.0 the Menu button is Kodi's "Context Menu". The Guide button is "PVR Device".
I used Logitech Harmony software to program the remote's Guide button back to Kodi's context menu (Logitech calls it DVDMenu)
I’m also having this same problem with both my “Menu” and “Guide” buttons on my Harmony 655 after upgrading to Kodi 18. I used the Keymap Editor app to reprogram my “Guide” button to Kodi’s “Context Menu”, but can’t find where the Kodi “Home” button is. Any ideas?