I just was trying to do an update on the production version of a site, pulling the code and replacing the database with a copy of the development db. The changes were pretty extensive - new modules, fields deleted and recreated as new field types, content types added, changed, and removed, etc. I'm using the dev-active / prod-active mirror config setup - dev-active is live on dev site, prod-active on prod site.
I found I had to manually make the prod-active config directory a copy of the dev-active config before loading the new database. I was unable to import changes. It would not change the existing fields, and it kept failing during import on settings files for new modules.
Does that sound normal? I thought I remembered it not being so much trouble, but I probably never made as many changes before.
I think that's what I had to do in the end. I haven't any similar problems since but I haven't made changes nearly as extensive, so.