Your lightmass settings are stored in the “world settings” of your persistent level. If you make any changes then you need to make them in both persistent levels. Persistent level is the one which is always loaded and contains all sub levels. This is where the world settings are stored. If you have everything in one level, then this is the persistent level.
So once you copied your old level and then deleted the doubled up content you also copied the world ssettings. When you made a new level and copied the content from the other level you didn’t copy the world settings. Hope that makes sense.
It helps when you look at it from the games perspective. Lets say you have a very detailed small indoor level and then you go outside to a very large less detailed outdoor area then you will need different lighting settings. That’s why they are stored per level and not project wide.