Formerly Logitech remote support for more than one box only worked for units using code 1 and code 2 (requires original remote to teach a command).
With thanks to AF123 (My Humax) who provided the required technical info.
Logitech now say all modes should work OK. I can confirm HDR1000S (Mode 1), HDR FOX T2 (mode 2) and second HDR FOX T2 (mode 3) all now work properly with my Harmony remote.
Interested to know how others using a Harmony remote get on with multiple units.