It’s started happening on a new blueprint in my project, and it actually seems to be tied to BlueprintLibrary function calls specifically (not internal function calls). Same deal as sample project I uploaded - remove function calls to BlueprintLibrary and you can then save without error.
This new case was on a brand new Blueprint Library, and a brand new Blueprint Actor - in 4.7.0 Preview 8.
Also, if file is having this problem DO NOT attempt to rename it. It’ll rename all references then delete blueprint without creating new renamed version. Found that out today and had to restore project from a backup since it was so broken.