Sometimes users stop seeing a file just because they unintentionally add a dot at the beginning of the name of that file.
Dolphin users had it solved in https://phabricator.kde.org/D15980, in Krusader I tried adding a confirmation dialog, although there is a drawback: after the renaming, if the confirmation dialog has been shown, then the focus is moved (that can be checked e.g. moving the up arrow key). Perhaps someone can solve that easily.