I've had the same issue recently. With one of the new versions of Atom, a setting was enabled that I had never changed, causing some files to not show up any more.
The setting is Hide VCS Ignored Files, which can be found in the Packages / Tree View settings:
Make sure this setting is disabled (i.e. unchecked). When it is checked, it will not show files that are ignored by Git. I noticed a .gitignore
file in your first screenshot - that could be causing it.
The setting one above this (Hide Ignored Names) could also be relevant, but I'm not entirely sure what it does.
Anyway, the Hide VCS Ignored Files was enabled in one of my workspaces for some reason, and it caused a similar issue as you described. It's probably worth a try...