I couldn’t use setq and custom-set-variables to have org-refile shows list of newly set org-agenda-files. Started to solve, first suspect I found was when I learned about custom.el file. Custom variable set by defcustom will set custom value in custom.el. I reset all custom.el to nil to make sure that it doesn’t set custom variables under weird condition that I am not aware of. I reloaded Doom Emacs. Changed variables didn’t reflect in helpful-variable, and org-agenda-files was not set to nil — value shown in custom.