The issue is once you use C-u C-c C-d to remove the deadline with your
point on the same line as the deadline, that line is removed and the point
stays in the same place.  That means point is now on Task 2 so calling
`org-deadline' there will apply to Task 2.

I think the easiest solution is to just change the old deadline using C-c
C-d.  From the prompt you can just type . to change the date to today.
This seems easier than your current workflow and you won't have the same
issue.

See this page for more details on the date/time prompt, it's very versatile
- https://orgmode.org/manual/The-date_002ftime-prompt.html

On Tue, Sep 18, 2018 at 9:26 AM Benson Chu <bensonchu457@gmail.com> wrote:

>
>
> Remember to cover the basics, that is, what you expected to happen and
> what in fact did happen. You don't know how to make a good report? See
>
> https://orgmode.org/manual/Feedback.html#Feedback
>
> Your bug report will be posted to the Org mailing list.
> ------------------------------------------------------------------------
>
> I have a problem in org agenda. I have been able to reproduce this bug
> in a simple environment. This is an example org file:
>
> * TODO Task 1
> <Already existing deadline>
> * TODO Task 2
>
> When I open org agenda, and I realize the deadline is far into the
> past, I want to move the deadline to today. So, the easiest thing I can
> think to do is C-u C-c C-d to remove the deadline, and then C-c C-d to
> add the deadline again to make it today. However, when I do this, the
> new deadline gets added to the task below, so I end up with something
> like this:
>
> * TODO Task 1
> * TODO Task 2
> <New deadline>
>
> Is this the intended behavior? I think that org agenda expects the
> deadline location to remain the same, but instead it gets removed, and
> accidentally adds it to the next task, which is very annoying. A few
> tasks of mine have disappeared into my large agenda file, and I've had
> to go back digging through to re-find and deadline them because of
> this. Are there any workarounds? Thanks!
>
> Emacs : GNU Emacs 26.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.22.30)
> of 2018-07-05
> Package: Org mode version 9.1.9 (release_9.1.9-65-g5e4542 @
> /usr/share/emacs/26.1/lisp/org/)
>
> current state:
> ==============
> (setq
> org-src-mode-hook '(org-src-babel-configure-edit-buffer
> org-src-mode-configure-edit-buffer)
> org-after-todo-state-change-hook '(org-clock-out-if-current)
> org-metadown-hook '(org-babel-pop-to-session-maybe)
> org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
> org-agenda-files '("/home/<my-name>/<my-sync-drive>/org/test/test-bug.org
> ")
> org-mode-hook '(#[0 "\300\301\302\303\304$\207"
> [add-hook change-major-mode-hook org-show-block-all append local] 5]
> #[0 "\300\301\302\303\304$\207"
> [add-hook change-major-mode-hook org-babel-show-result-all append local] 5]
> org-babel-result-hide-spec org-babel-hide-all-hashes)
> org-archive-hook '(org-attach-archive-delete-maybe)
> org-confirm-elisp-link-function 'yes-or-no-p
> org-agenda-before-write-hook '(org-agenda-add-entry-text)
> org-metaup-hook '(org-babel-load-in-session-maybe)
> org-bibtex-headline-format-function #[257 "\300.\236A\207" [:title] 3
> "\n\n(fn ENTRY)"]
> org-babel-pre-tangle-hook '(save-buffer)
> org-tab-first-hook '(org-babel-hide-result-toggle-maybe
> org-babel-header-arg-expand)
> org-occur-hook '(org-first-headline-recenter)
> org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
> org-cycle-show-empty-lines
> org-optimize-window-after-visibility-change)
> org-speed-command-hook '(org-speed-command-activate
> org-babel-speed-command-activate)
> org-confirm-shell-link-function 'yes-or-no-p
> org-link-parameters '(("id" :follow org-id-open)
> ("rmail" :follow org-rmail-open :store org-rmail-store-link)
> ("mhe" :follow org-mhe-open :store org-mhe-store-link)
> ("irc" :follow org-irc-visit :store org-irc-store-link)
> ("info" :follow org-info-open :export org-info-export :store
> org-info-store-link)
> ("gnus" :follow org-gnus-open :store org-gnus-store-link)
> ("docview" :follow org-docview-open :export org-docview-export :store
> org-docview-store-link)
> ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
> ("bbdb" :follow org-bbdb-open :export org-bbdb-export :complete
> org-bbdb-complete-link :store org-bbdb-store-link)
> ("w3m" :store org-w3m-store-link) ("file+sys") ("file+emacs")
> ("doi" :follow org--open-doi-link) ("elisp" :follow org--open-elisp-link)
> ("file" :complete org-file-complete-link)
> ("ftp" :follow (lambda (path) (browse-url (concat "ftp:" path))))
> ("help" :follow org--open-help-link)
> ("http" :follow (lambda (path) (browse-url (concat "http:" path))))
> ("https" :follow (lambda (path) (browse-url (concat "https:" path))))
> ("mailto" :follow (lambda (path) (browse-url (concat "mailto:" path))))
> ("news" :follow (lambda (path) (browse-url (concat "news:" path))))
> ("shell" :follow org--open-shell-link))
> )
>
>
>

-- 
Thanks,
Kevin Foley