Startup settings, like the new technologies or recipes, can only be changed at Startup unfortunately. This is sadly a limitation of the way Factorio mods work.
If you remove a mod from the save, load the factory and save a new copy, then reinstall the mod with the startup settings you want it may work via the migration scripts, but this will have consequences like buildings losing their set recipes in some cases as an example. It's a bit tedious but it might work for you.
