In case anyone else has this nightmare of a problem, here are some things I learnt in the process of sorting out my mess.
1. Have a very clear idea long term of your keyword structure and try very hard to stick to it. Making changes later can be arduous.
2. Keywords are heirarchical. Remove all sub-keywords before removing a keyword.
3. Keywords in italics are those that have been found in your meta and are not declared by you. Deleting these keywords should remove them from the metadata, I recommend you check.
4. If you are making selections of PSD files make them broad. Use top level keywords and then use sub-keywords later when you are working on jpgs.
- When you see Bridge processing changes in the workspace footer, I recommend you pause making any further changes until it has caught up with you.
- In the first attempt at this I made all of the above mistakes and to clear out the mess I had to go folder by folder removing keywords until I had cleaned up my mess. I wish I had understood better how the system works, because it is so flakey and it is so hard to make any corrections.
- If you get your keyword design wrong you will have Collections that load painfully slowly.
- I recommend your scratch drive being M.2, large and reliable.
I hope this helps someone because I have spent long, dreary days working all of this out and fixing it!
Good luck.