Cannot get AJAX callback values to save
That code is overriding the fields structure. That fields have a specific structure and that code is changing it completely, so in submit the values are not recognized. 

I recommend you use devel module and use dpm function to inspect the structure of that fields:

  dpm($form['field_cr_case_number']);
  dpm($form['field_cr_case_title']);


To make your form changes you must only add the #ajax property to your field:

$form['field_cr_case_number'][LANGUAGE_NONE][0]['value']['#ajax'] = array(
  'callback' =&gt; 'case_records_database_ajax_callback',
  'event' =&gt; 'change',
  'method' =&gt; 'replace',
  'wrapper' =&gt; 'div-case-name-element-wrapper',
);


And to add the wrapper and #value to your second field do something like this:

$form['field_cr_case_title'][LANGUAGE_NONE][0]['value']['#prefix'] = '&lt;div id="div-case-name-element-wrapper"&gt;';
$form['field_cr_case_title'][LANGUAGE_NONE][0]['value']['#suffix'] = '&lt;/div&gt;';
$form['field_cr_case_title'][LANGUAGE_NONE][0]['value']['#value'] = $cs_short_title;


In this question is also explained how to make the ajax callback.