Various issues when switching branches on Git


I’m facing various issues when switching branches on Git. A significant issue is that files disappear after leaving and returning to a branch. For example. For example, here you can see the components folder in windows explorer next to the folder in Atom. The missing files are marked.

Also Atom doesn’t always follow changes in files when changing a branch etc, which causes many problems later with Git. The issue doesn’t seem to be coming from Git as I used a few different Git programs (Git Kraken, Git from Bash, and Sorucetree}.
I tried reinstalling Atom. I also disabled all packages besides core packages and Atom-beautify and language-Babel.
Is it a known-issue? Suggestions?


Here is some more information. I’m using Windows 10 (with the Creators update), and latest version of Atom. Atom shows it’s in the right branch (Dev) and those missing files are an essential part of the app and should be there.
The files don’t show in Atom’s file tree, but they are open in Atom as if I didn’t leave master.

The only solution I can find is to close Atom and to select Don’t Save regarding all of those missing files.


When I try to go back to master I’m facing an issue in Git

This is an odd behavior as the wroking directory shows no changes. I can’t paste another image (new user) but Sourcetree shows an empty working directory. The screenshot above is from Sourcetree but I was facing a similar issue with GitKraken.
After restarting the computer all the missing files, are shown in the working directory as deleted.
Sorry about posting a few messages I wanted to provide many details.