Similar issue here, Only I also do use 'Loot' for sorting. (which can create its own issues if one is not careful) But in my case, I found that the "spring cleaning - compatibility patch" had some-how been dropped or otherwise deactivated. I re-activated it, In NMM , and made sure it was last in the load order. Then I loaded the last save prior to my finding the "returned / regenerated" buildings in Sanctuary, and Presto! They are gone again! Much thanks folks !!