@ChimpsInTies
OK I got the external hard drive working which does seem like a better way to go, however the internal sd card share still didn't reduce in size and is 100% full. I thought it was move the files over to the external drive but it appears to have just copied them. This also means I have 2 copies of some games. Bit strange. Maybe it's expected behaviour, I don't know?
I ended up unplugging the extrnal drive, then accessing the sd card share and deleting all the previously crated kodi images and the games on there. Now it's got some space and everything is stored on the external drive.
This still didn't answer the question as to why I only ended up with a tiny 3.2GB share partition in the first place but at least it's working now. I've realised that once you get to scraping your games and it downloads screenshots and videos it does start to take up a lot of space anyway so probably good to have 2TB instead