Steps to replicate.
1. Evaluate the following:
(setq org-time-stamp-custom-formats '("<%B %e, %Y>" . "<%B %e, %Y>"))
2. Use the following sample org file.
--8<---------------cut here---------------start------------->8---
#+DATE: [2014-07-30 Wed 22:05]
* Headline
[2014-07-30 Wed 22:05]
--8<---------------cut here---------------end--------------->8---
3. M-x org-toggle-time-stamp-overlays
The buffer should look like this:
--8<---------------cut here---------------start------------->8---
#+DATE: [2014-07-30 Wed]
* Headline
[2014-07-30 Wed]
--8<---------------cut here---------------end--------------->8---
4. M-x org-toggle-time-stamp-overlays
The buffer now looks like this:
--8<---------------cut here---------------start------------->8---
#+DATE: [2014-07-30 Wed 22:05]
* Headline
[2014-07-30 Wed 22:05]
--8<---------------cut here---------------end--------------->8---
...thus preventing any easy editing of the timestamp in the #+DATE
line.
Best,
Matt