I just wanted to add that I experience this issue as well. My case may be a bit different however.
I have a project on Windows, using the 4.12.0 binary editor. When I copy over this project to Mac and proceed to open it with either the source or binary version of 4.12.0, the external references warning will pop up. This is a serious problem, as packaging with this warning prevents the maps or assets from being included in the packaged build.
I have also tested this in 4.12.1 and 4.12.2 with the same outcome. The project was initially on Windows under version 4.10.4. After upgrading it to 4.12, this issue has come about. It’s not the first time though, bringing anything from Window’s editor over to the Mac editor always produced this problem. Only now, we can no longer solve it by the renaming the folder trick.
Doing a clean copy via editor, or an in-place conversion does not change the outcome either. Neither does removing the folders Intermediate, Saved, Build or Binaries.