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