OK thanks so much for some input. I've done a fair bit of testing today, especially after Paul's comments, as otherwise I'd have given up on Emby, at least for Kodi. Paul is right, you can use the nfo files to update Emby.
So that it is written somewhere, there are three options when you go to the Refresh Metadata item. I set up two TV shows with different tags to the online version, and then added a TestNFO tag to the nfo files.
Scan for new and updated files - not overly sure what this does as I had no new shows. Although I had clearly modifed two, but it altered nothing.
Search for missing metadata - this is as Paul suggested the way to use nfo files to update Emby. It will overwrite shows Locked in Emby.
Replace all metadata - this changes the Emby metadata from online.
So none of these altered existing nfo files. However it was Emby which created them in the first place so it can be done, possilbly when you check the NFO option when creating a library.
Anyway, this keeps my hopes and dreams alive, although I can't really see any advantage to using Kodi via Emby over just using a direct connection. Kodi is slower now, less responsive. It crashes a lot. It's all Beta of course, so who knows if it will work eventually.
And feerlessldr, thanks but the Metadata Manager is no use for bulk updating. I have hundreds of TV shows and more movies. Having to go to each one individually to clear genres is hard. Harder if I am then going to reapply my own. Especially as there is so much metadata to sift through, and genres being in the middle, it is quite tricky each time. You then have to go back to the top or bottom to save. I can write software to update nfo files in bulk, so I will. After I check out Tiny Media Manager.
So Emby people, I have read so many of these forums and it seems to me that sorting out metadata is a bit of an in-joke for you. You seem to delight in popping in to the forums to say that it's on the agenda. But I think it is something you are close to being good at. For example, a filtering system on the Metadata Manager page so that one could hide any of the Main data, Genres, Actors, Studio, etc. So you could go through and just look at the ones you cared about. That would make it usable. The page is about four screens tall. And if you could make changes at folder level and propogate them down, then you're basically there. As a developer I get that the last one is a little trickly as you have some ways of going about it and some of them make it hard to get the UI right. But it is doable if you think clearly enough about it.
Thanks again all. I'll let you know how I get on.