I use github desktop. I was working on my branch and at one time I needed to upgrade my MAMP to MAMP PRO. In MAMP PRO I needed to set up new localserver with SSL. When setting up new server I needed to change access rights for directory and files. After making change my Github desktop shows all files that weren't changed as changed (in the right panel which shows changes is empty), files that were changed are not shown in git desktop and versions of files locally are old (before changes).
Git desktop is currently showing "branch A", but when I checked in terminal, it showed that currently master is shown. At one moment when I tried to change to my desired "branch A", git opened error: fatal: Unable to create '.../.git/index.lock': Permission denied (128)
After a little research I figured out that changing permissions have made Git desktop act strange. How to get it back with my uncommitted changes from "Branch A"?
You can simply try removing the lock file using git shell.
Also please try running github for desktop with admin privileges.