Update: CocoaPods 0.28.0 appears to have resolved this issue.
Are you using CocoaPods to manage your dependencies? It's possible a recent update has caused this.
I encountered the same issue with a universal app recently. Image sets that included separate, device-specific resources only included assets for a single device type after build. I similarly had made no apparent changes to the project around these assets and my storyboards appeared correct.
After Googling around, I discovered issues with Asset Catalogs reported on the main CocoaPods project (https://github.com/CocoaPods/CocoaPods/issues/1520) and realised that perhaps updating CocoaPods could be the change that wasn't apparent.
Rolling back my installation of CocoaPods from 0.27.1 to 0.26.2, the release before support was included for compiling xcassets in Pod dependencies, appears to have fixed this issue for now. I'll be keeping an eye on upcoming releases as it seems there is very active development in this area.