I'm sorry for my previous comments.
I don't know why it didn't work, but currently I fixed that problem with following steps:
- Go to Project Target -> Info and then delete KeyValue object for key Main storyboard file base name and Main storyboard file base name (iPad).
- To ensure that it's completely removed, go to Info.plist file and verify the KeyValue objects aren't exist there. If they are, then also delete from there.
- Remove references to Storyboards from Xcode project.
- Add Storyboards back to the project by right-click on the project in Xcode -> Add files to project_name, tick the Copy items if needed, Create groups and project target options.
- Set Storyboards names both for iPhone and iPad in Project Target –> Info, by adding previously removed KeyValue objects.
From now Storyboards work as previously!