So, Update on this,
I went ahead and fully programmed the unit as suggested, fine, it can read the addresses for the points and switch them correctly, so I'm happy with that unit.
The second unit I needed to program, plugged in straight away and flashed as stated in the DCC Next manual, eventually got this all programmed as well.
All in all, everything is working as it should, I'm just slightly confused regarding one unit flashing and the other, doesn't matter however, they are all programmed and working.
Thanks for all your help.