If you didn't know, there are two methods of archiving subtrees in Emacs' Org-mode.
I often use the latter but the issue here is that all my items got disappeared from Org Agenda view when archived.
You can tell Org Agenda to show archived records by pressing `v A` in `*Org Agenda*` buffer. Notice upper-cased `A`. If you use lowercase `a` then only internally archived records will be shown.
What `v A` does is it calling `(org-agenda-archives-mode 'files)` which internally sets `org-agenda-archives-mode` variable to `t`.
This is what we can do in our `init.el`:
(setq org-agenda-archives-mode t)
Done!