Org-mode stores archived TODOs from todo.org into todo.org_archive. It also
creates .org-id-locations in some cases.

The behavior is documented in [1].
The prefix doesn't seem to be documented, but it is hardoced as described in [2].

[1]: http://www.gnu.org/software/emacs/manual/html_node/emacs/Interlocking.html#Interlocking
[2]: http://tekman.livejournal.com/79598.html