Atom 1.22 on Windows 10. Right click on tree view, select delete. File is still in tree and on disk. Just like Atom bugs #666 and #6064.
Ah. Here was the problem. The file was still open in PDF reader, on another workspace. The bug here is that Atom does not report failure on deleting.
Curios if there’s any error in devtools (Ctrl+Shift+I) in the Consle tab?