First, we have to stop the currently running skhd process. We can do that with brew command.
brew services stop skhd
After this we can run skhd in verbose mode with skhd -V
~ ᐅ skhd -V
skhd: successfully created pid-file..
skhd: secure keyboard entry is enabled by (5530) 'iterm2'! abort..
After googling around, I found out that on “iTerm” the “secure keyboard entry” was enabled somehow. Probably it got enabled because of me hitting random keyboard shortcuts while trying to find some shortcuts.
After this I disabled Secure Keyboard Entry from iTerm menu and then skhd keyboard shortcuts started working again.