I am also seeing something similar with B4 on Windows.
I use git as source control so files are changing regularly as I change branches.
After changing the branch, occasionally but not always, some of the files will disappear from the view.
If I click "refresh" on the project, the files reappear.
All files are local, on an NTFS disk, if it matters.
Any other information that would be useful? Is this different enough from the issue in this thread I should start another one?